From 0203a69d88c854c1fe3a210c83ff3ee0d943f4df Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Thu, 19 Nov 2015 20:21:41 -0500 Subject: [PATCH] Tours. --- client/bower.json | 1 + client/galaxy/scripts/apps/analysis.js | 32 +- client/galaxy/scripts/layout/menu.js | 40 +- client/galaxy/scripts/libs/bootstrap-tour.js | 802 ++++++++++++++++++ .../scripts/mvc/tool/tool-form-composite.js | 2 +- client/galaxy/scripts/mvc/tours.js | 62 ++ .../scripts/mvc/upload/upload-button.js | 2 +- .../less/galaxy_bootstrap/variables.less | 2 +- client/grunt-tasks/install-libs.js | 3 +- config/galaxy.ini.sample | 4 + lib/galaxy/app.py | 3 + lib/galaxy/config.py | 2 + lib/galaxy/tours/__init__.py | 59 ++ lib/galaxy/webapps/galaxy/api/tours.py | 34 + lib/galaxy/webapps/galaxy/buildapp.py | 16 + static/maps/galaxy.menu.js.map | 1 + static/maps/layout/menu.js.map | 2 +- static/maps/libs/bootstrap-tour.js.map | 1 + static/maps/mvc/tours.js.map | 1 + static/maps/mvc/upload/upload-button.js.map | 2 +- static/scripts/bundled/analysis.bundled.js | 17 +- .../scripts/bundled/analysis.bundled.js.map | 2 +- static/scripts/bundled/libs.bundled.js | 32 +- static/scripts/bundled/libs.bundled.js.map | 2 +- static/scripts/galaxy.menu.js | 2 + static/scripts/layout/menu.js | 2 +- static/scripts/libs/bootstrap-tour.js | 2 + static/scripts/mvc/tours.js | 2 + static/scripts/mvc/upload/upload-button.js | 2 +- static/style/blue/base.css | 2 +- static/style/blue/bootstrap-tour.css | 728 ++++++++++++++++ templates/base.mako | 2 + templates/base/base_panels.mako | 2 +- 33 files changed, 1820 insertions(+), 48 deletions(-) create mode 100644 client/galaxy/scripts/libs/bootstrap-tour.js create mode 100644 client/galaxy/scripts/mvc/tours.js create mode 100644 lib/galaxy/tours/__init__.py create mode 100644 lib/galaxy/webapps/galaxy/api/tours.py create mode 100644 static/maps/galaxy.menu.js.map create mode 100644 static/maps/libs/bootstrap-tour.js.map create mode 100644 static/maps/mvc/tours.js.map create mode 100644 static/scripts/galaxy.menu.js create mode 100644 static/scripts/libs/bootstrap-tour.js create mode 100644 static/scripts/mvc/tours.js create mode 100755 static/style/blue/bootstrap-tour.css diff --git a/client/bower.json b/client/bower.json index 67262e323ab..28c80b4bb62 100644 --- a/client/bower.json +++ b/client/bower.json @@ -14,6 +14,7 @@ "underscore": "~1.7.0", "backbone": "~1.1.2", "bootstrap": "~3.3.2", + "bootstrap-tour":"~0.10.2", "d3": "~3.5.3", "farbtastic": "~2.0.0-alpha.1", "toastr": "~2.1.0", diff --git a/client/galaxy/scripts/apps/analysis.js b/client/galaxy/scripts/apps/analysis.js index 5195fc73afc..c32ea42f0dd 100644 --- a/client/galaxy/scripts/apps/analysis.js +++ b/client/galaxy/scripts/apps/analysis.js @@ -7,7 +7,8 @@ var jQuery = require( 'jquery' ), ToolPanel = require( './tool-panel' ), HistoryPanel = require( './history-panel' ), PAGE = require( 'layout/page' ), - ToolForm = require( 'mvc/tool/tool-form' ); + ToolForm = require( 'mvc/tool/tool-form' ), + Tours = require('libs/bootstrap-tour'); /** define the 'Analyze Data'/analysis/main/home page for Galaxy * * has a masthead @@ -75,6 +76,35 @@ window.app = function app( options, bootstrapped ){ $( '.select2-hidden-accessible' ).remove(); centerPanel.display( view ); }, + // DBTODO: THIS SHOULD PROBABLY NOT BE HERE -- but where? + giveTour: function(tour_id){ + var url = Galaxy.root + 'api/tours/' + tour_id; + $.getJSON( url, function( data ) { + // Set hooks for additional click and data entry actions. + _.each(data.steps, function(step) { + if (step.preclick){ + step.onShow= function(){$(step.preclick).click()}; + } + if (step.postclick){ + step.onHide = function(){$(step.postclick).click()}; + } + if (step.textinsert){ + step.onShown= function(){$(step.element).text(step.textinsert)}; + } + }); + // Store tour steps in sessionStorage to easily persist w/o hackery. + sessionStorage.setItem('activeGalaxyTour', data); + var tour = new Tour({ + orphan: true, + debug: true, // REMOVE ME WHEN DONE DEBUGGING + steps: data.steps + }); + // Always clean restart, since this is a new, explicit giveTour execution. + tour.init(); + tour.goTo(0); + tour.restart(); + }); + }, }; // .................................................... routes diff --git a/client/galaxy/scripts/layout/menu.js b/client/galaxy/scripts/layout/menu.js index d19b259fbe7..fe57e1ff0aa 100644 --- a/client/galaxy/scripts/layout/menu.js +++ b/client/galaxy/scripts/layout/menu.js @@ -1,5 +1,5 @@ // dependencies -define([], function() { +define(['mvc/tours'], function( Tours ) { /** GalaxyMenu uses the GalaxyMasthead class in order to add menu items and icons to the Masthead **/ var GalaxyMenu = Backbone.Model.extend({ @@ -81,6 +81,7 @@ var GalaxyMenu = Backbone.Model.extend({ content : 'page/list_published' }); + this.masthead.append(tab_shared); // @@ -209,6 +210,13 @@ var GalaxyMenu = Backbone.Model.extend({ target : '_blank' }); } + tab_help.add({ + title : 'Interactive Tours', + onclick : function(c){ + Galaxy.app.display(new Tours.ToursView()); + }, + target : 'galaxy_main' + }); this.masthead.append( tab_help ); // @@ -388,7 +396,8 @@ var GalaxyMastheadTab = Backbone.View.extend({ type : 'url', target : '_parent', scratchbook : false, - divider : false + divider : false, + onclick : undefined } // read in defaults @@ -419,17 +428,26 @@ var GalaxyMastheadTab = Backbone.View.extend({ // add events var self = this; - $item.on('click', function(e){ - // prevent default - e.preventDefault(); - // no modifications if new tab is requested - if (self.options.target === '_blank') - return true; - // load into frame - Galaxy.frame.add(options); - }); + if (menuOptions.onclick !== undefined){ + $item.on('click', function(e){ + e.preventDefault(); + menuOptions.onclick(); + }); + } else { + $item.on('click', function(e){ + // prevent default + e.preventDefault(); + + // no modifications if new tab is requested + if (self.options.target === '_blank') + return true; + + // load into frame + Galaxy.frame.add(options); + }); + } // append divider if (menuOptions.divider) diff --git a/client/galaxy/scripts/libs/bootstrap-tour.js b/client/galaxy/scripts/libs/bootstrap-tour.js new file mode 100644 index 00000000000..1874061e8cd --- /dev/null +++ b/client/galaxy/scripts/libs/bootstrap-tour.js @@ -0,0 +1,802 @@ +/* ======================================================================== + * bootstrap-tour - v0.10.1 + * http://bootstraptour.com + * ======================================================================== + * Copyright 2012-2013 Ulrich Sossou + * + * ======================================================================== + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== + */ + +(function($, window) { + var Tour, document; + document = window.document; + Tour = (function() { + function Tour(options) { + var storage; + try { + storage = window.localStorage; + } catch (_error) { + storage = false; + } + this._options = $.extend({ + name: 'tour', + steps: [], + container: 'body', + autoscroll: true, + keyboard: true, + storage: storage, + debug: false, + backdrop: false, + backdropPadding: 0, + redirect: true, + orphan: false, + duration: false, + delay: false, + basePath: '', + template: '', + afterSetState: function(key, value) {}, + afterGetState: function(key, value) {}, + afterRemoveState: function(key) {}, + onStart: function(tour) {}, + onEnd: function(tour) {}, + onShow: function(tour) {}, + onShown: function(tour) {}, + onHide: function(tour) {}, + onHidden: function(tour) {}, + onNext: function(tour) {}, + onPrev: function(tour) {}, + onPause: function(tour, duration) {}, + onResume: function(tour, duration) {} + }, options); + this._force = false; + this._inited = false; + this.backdrop = { + overlay: null, + $element: null, + $background: null, + backgroundShown: false, + overlayElementShown: false + }; + this; + } + + Tour.prototype.addSteps = function(steps) { + var step, _i, _len; + for (_i = 0, _len = steps.length; _i < _len; _i++) { + step = steps[_i]; + this.addStep(step); + } + return this; + }; + + Tour.prototype.addStep = function(step) { + this._options.steps.push(step); + return this; + }; + + Tour.prototype.getStep = function(i) { + if (this._options.steps[i] != null) { + return $.extend({ + id: "step-" + i, + path: '', + placement: 'right', + title: '', + content: '

', + next: i === this._options.steps.length - 1 ? -1 : i + 1, + prev: i - 1, + animation: true, + container: this._options.container, + autoscroll: this._options.autoscroll, + backdrop: this._options.backdrop, + backdropPadding: this._options.backdropPadding, + redirect: this._options.redirect, + orphan: this._options.orphan, + duration: this._options.duration, + delay: this._options.delay, + template: this._options.template, + onShow: this._options.onShow, + onShown: this._options.onShown, + onHide: this._options.onHide, + onHidden: this._options.onHidden, + onNext: this._options.onNext, + onPrev: this._options.onPrev, + onPause: this._options.onPause, + onResume: this._options.onResume + }, this._options.steps[i]); + } + }; + + Tour.prototype.init = function(force) { + this._force = force; + if (this.ended()) { + this._debug('Tour ended, init prevented.'); + return this; + } + this.setCurrentStep(); + this._initMouseNavigation(); + this._initKeyboardNavigation(); + this._onResize((function(_this) { + return function() { + return _this.showStep(_this._current); + }; + })(this)); + if (this._current !== null) { + this.showStep(this._current); + } + this._inited = true; + return this; + }; + + Tour.prototype.start = function(force) { + var promise; + if (force == null) { + force = false; + } + if (!this._inited) { + this.init(force); + } + if (this._current === null) { + promise = this._makePromise(this._options.onStart != null ? this._options.onStart(this) : void 0); + this._callOnPromiseDone(promise, this.showStep, 0); + } + return this; + }; + + Tour.prototype.next = function() { + var promise; + promise = this.hideStep(this._current); + return this._callOnPromiseDone(promise, this._showNextStep); + }; + + Tour.prototype.prev = function() { + var promise; + promise = this.hideStep(this._current); + return this._callOnPromiseDone(promise, this._showPrevStep); + }; + + Tour.prototype.goTo = function(i) { + var promise; + promise = this.hideStep(this._current); + return this._callOnPromiseDone(promise, this.showStep, i); + }; + + Tour.prototype.end = function() { + var endHelper, promise; + endHelper = (function(_this) { + return function(e) { + $(document).off("click.tour-" + _this._options.name); + $(document).off("keyup.tour-" + _this._options.name); + $(window).off("resize.tour-" + _this._options.name); + _this._setState('end', 'yes'); + _this._inited = false; + _this._force = false; + _this._clearTimer(); + if (_this._options.onEnd != null) { + return _this._options.onEnd(_this); + } + }; + })(this); + promise = this.hideStep(this._current); + return this._callOnPromiseDone(promise, endHelper); + }; + + Tour.prototype.ended = function() { + return !this._force && !!this._getState('end'); + }; + + Tour.prototype.restart = function() { + this._removeState('current_step'); + this._removeState('end'); + return this.start(); + }; + + Tour.prototype.pause = function() { + var step; + step = this.getStep(this._current); + if (!(step && step.duration)) { + return this; + } + this._paused = true; + this._duration -= new Date().getTime() - this._start; + window.clearTimeout(this._timer); + this._debug("Paused/Stopped step " + (this._current + 1) + " timer (" + this._duration + " remaining)."); + if (step.onPause != null) { + return step.onPause(this, this._duration); + } + }; + + Tour.prototype.resume = function() { + var step; + step = this.getStep(this._current); + if (!(step && step.duration)) { + return this; + } + this._paused = false; + this._start = new Date().getTime(); + this._duration = this._duration || step.duration; + this._timer = window.setTimeout((function(_this) { + return function() { + if (_this._isLast()) { + return _this.next(); + } else { + return _this.end(); + } + }; + })(this), this._duration); + this._debug("Started step " + (this._current + 1) + " timer with duration " + this._duration); + if ((step.onResume != null) && this._duration !== step.duration) { + return step.onResume(this, this._duration); + } + }; + + Tour.prototype.hideStep = function(i) { + var hideStepHelper, promise, step; + step = this.getStep(i); + if (!step) { + return; + } + this._clearTimer(); + promise = this._makePromise(step.onHide != null ? step.onHide(this, i) : void 0); + hideStepHelper = (function(_this) { + return function(e) { + var $element; + $element = $(step.element); + if (!($element.data('bs.popover') || $element.data('popover'))) { + $element = $('body'); + } + $element.popover('destroy').removeClass("tour-" + _this._options.name + "-element tour-" + _this._options.name + "-" + i + "-element"); + if (step.reflex) { + $element.removeClass('tour-step-element-reflex').off("" + (_this._reflexEvent(step.reflex)) + ".tour-" + _this._options.name); + } + if (step.backdrop) { + _this._hideBackdrop(); + } + if (step.onHidden != null) { + return step.onHidden(_this); + } + }; + })(this); + this._callOnPromiseDone(promise, hideStepHelper); + return promise; + }; + + Tour.prototype.showStep = function(i) { + var promise, showStepHelper, skipToPrevious, step; + if (this.ended()) { + this._debug('Tour ended, showStep prevented.'); + return this; + } + step = this.getStep(i); + if (!step) { + return; + } + skipToPrevious = i < this._current; + promise = this._makePromise(step.onShow != null ? step.onShow(this, i) : void 0); + showStepHelper = (function(_this) { + return function(e) { + var current_path, path, showPopoverAndOverlay; + _this.setCurrentStep(i); + path = (function() { + switch ({}.toString.call(step.path)) { + case '[object Function]': + return step.path(); + case '[object String]': + return this._options.basePath + step.path; + default: + return step.path; + } + }).call(_this); + current_path = [document.location.pathname, document.location.hash].join(''); + if (_this._isRedirect(path, current_path)) { + _this._redirect(step, path); + return; + } + if (_this._isOrphan(step)) { + if (!step.orphan) { + _this._debug("Skip the orphan step " + (_this._current + 1) + ".\nOrphan option is false and the element does not exist or is hidden."); + if (skipToPrevious) { + _this._showPrevStep(); + } else { + _this._showNextStep(); + } + return; + } + _this._debug("Show the orphan step " + (_this._current + 1) + ". Orphans option is true."); + } + if (step.backdrop) { + _this._showBackdrop(!_this._isOrphan(step) ? step.element : void 0); + } + showPopoverAndOverlay = function() { + if (_this.getCurrentStep() !== i) { + return; + } + if ((step.element != null) && step.backdrop) { + _this._showOverlayElement(step); + } + _this._showPopover(step, i); + if (step.onShown != null) { + step.onShown(_this); + } + return _this._debug("Step " + (_this._current + 1) + " of " + _this._options.steps.length); + }; + if (step.autoscroll) { + _this._scrollIntoView(step.element, showPopoverAndOverlay); + } else { + showPopoverAndOverlay(); + } + if (step.duration) { + return _this.resume(); + } + }; + })(this); + if (step.delay) { + this._debug("Wait " + step.delay + " milliseconds to show the step " + (this._current + 1)); + window.setTimeout((function(_this) { + return function() { + return _this._callOnPromiseDone(promise, showStepHelper); + }; + })(this), step.delay); + } else { + this._callOnPromiseDone(promise, showStepHelper); + } + return promise; + }; + + Tour.prototype.getCurrentStep = function() { + return this._current; + }; + + Tour.prototype.setCurrentStep = function(value) { + if (value != null) { + this._current = value; + this._setState('current_step', value); + } else { + this._current = this._getState('current_step'); + this._current = this._current === null ? null : parseInt(this._current, 10); + } + return this; + }; + + Tour.prototype._setState = function(key, value) { + var e, keyName; + if (this._options.storage) { + keyName = "" + this._options.name + "_" + key; + try { + this._options.storage.setItem(keyName, value); + } catch (_error) { + e = _error; + if (e.code === DOMException.QUOTA_EXCEEDED_ERR) { + this._debug('LocalStorage quota exceeded. State storage failed.'); + } + } + return this._options.afterSetState(keyName, value); + } else { + if (this._state == null) { + this._state = {}; + } + return this._state[key] = value; + } + }; + + Tour.prototype._removeState = function(key) { + var keyName; + if (this._options.storage) { + keyName = "" + this._options.name + "_" + key; + this._options.storage.removeItem(keyName); + return this._options.afterRemoveState(keyName); + } else { + if (this._state != null) { + return delete this._state[key]; + } + } + }; + + Tour.prototype._getState = function(key) { + var keyName, value; + if (this._options.storage) { + keyName = "" + this._options.name + "_" + key; + value = this._options.storage.getItem(keyName); + } else { + if (this._state != null) { + value = this._state[key]; + } + } + if (value === void 0 || value === 'null') { + value = null; + } + this._options.afterGetState(key, value); + return value; + }; + + Tour.prototype._showNextStep = function() { + var promise, showNextStepHelper, step; + step = this.getStep(this._current); + showNextStepHelper = (function(_this) { + return function(e) { + return _this.showStep(step.next); + }; + })(this); + promise = this._makePromise(step.onNext != null ? step.onNext(this) : void 0); + return this._callOnPromiseDone(promise, showNextStepHelper); + }; + + Tour.prototype._showPrevStep = function() { + var promise, showPrevStepHelper, step; + step = this.getStep(this._current); + showPrevStepHelper = (function(_this) { + return function(e) { + return _this.showStep(step.prev); + }; + })(this); + promise = this._makePromise(step.onPrev != null ? step.onPrev(this) : void 0); + return this._callOnPromiseDone(promise, showPrevStepHelper); + }; + + Tour.prototype._debug = function(text) { + if (this._options.debug) { + return window.console.log("Bootstrap Tour '" + this._options.name + "' | " + text); + } + }; + + Tour.prototype._isRedirect = function(path, currentPath) { + return (path != null) && path !== '' && (({}.toString.call(path) === '[object RegExp]' && !path.test(currentPath)) || ({}.toString.call(path) === '[object String]' && path.replace(/\?.*$/, '').replace(/\/?$/, '') !== currentPath.replace(/\/?$/, ''))); + }; + + Tour.prototype._redirect = function(step, path) { + if ($.isFunction(step.redirect)) { + return step.redirect.call(this, path); + } else if (step.redirect === true) { + this._debug("Redirect to " + path); + return document.location.href = path; + } + }; + + Tour.prototype._isOrphan = function(step) { + return (step.element == null) || !$(step.element).length || $(step.element).is(':hidden') && ($(step.element)[0].namespaceURI !== 'http://www.w3.org/2000/svg'); + }; + + Tour.prototype._isLast = function() { + return this._current < this._options.steps.length - 1; + }; + + Tour.prototype._showPopover = function(step, i) { + var $element, $tip, isOrphan, options; + $(".tour-" + this._options.name).remove(); + options = $.extend({}, this._options); + isOrphan = this._isOrphan(step); + step.template = this._template(step, i); + if (isOrphan) { + step.element = 'body'; + step.placement = 'top'; + } + $element = $(step.element); + $element.addClass("tour-" + this._options.name + "-element tour-" + this._options.name + "-" + i + "-element"); + if (step.options) { + $.extend(options, step.options); + } + if (step.reflex && !isOrphan) { + $element.addClass('tour-step-element-reflex'); + $element.off("" + (this._reflexEvent(step.reflex)) + ".tour-" + this._options.name); + $element.on("" + (this._reflexEvent(step.reflex)) + ".tour-" + this._options.name, (function(_this) { + return function() { + if (_this._isLast()) { + return _this.next(); + } else { + return _this.end(); + } + }; + })(this)); + } + $element.popover({ + placement: step.placement, + trigger: 'manual', + title: step.title, + content: step.content, + html: true, + animation: step.animation, + container: step.container, + template: step.template, + selector: step.element + }).popover('show'); + $tip = $element.data('bs.popover') ? $element.data('bs.popover').tip() : $element.data('popover').tip(); + $tip.attr('id', step.id); + this._reposition($tip, step); + if (isOrphan) { + return this._center($tip); + } + }; + + Tour.prototype._template = function(step, i) { + var $navigation, $next, $prev, $resume, $template; + $template = $.isFunction(step.template) ? $(step.template(i, step)) : $(step.template); + $navigation = $template.find('.popover-navigation'); + $prev = $navigation.find('[data-role="prev"]'); + $next = $navigation.find('[data-role="next"]'); + $resume = $navigation.find('[data-role="pause-resume"]'); + if (this._isOrphan(step)) { + $template.addClass('orphan'); + } + $template.addClass("tour-" + this._options.name + " tour-" + this._options.name + "-" + i); + if (step.prev < 0) { + $prev.addClass('disabled'); + } + if (step.next < 0) { + $next.addClass('disabled'); + } + if (!step.duration) { + $resume.remove(); + } + return $template.clone().wrap('
').parent().html(); + }; + + Tour.prototype._reflexEvent = function(reflex) { + if ({}.toString.call(reflex) === '[object Boolean]') { + return 'click'; + } else { + return reflex; + } + }; + + Tour.prototype._reposition = function($tip, step) { + var offsetBottom, offsetHeight, offsetRight, offsetWidth, originalLeft, originalTop, tipOffset; + offsetWidth = $tip[0].offsetWidth; + offsetHeight = $tip[0].offsetHeight; + tipOffset = $tip.offset(); + originalLeft = tipOffset.left; + originalTop = tipOffset.top; + offsetBottom = $(document).outerHeight() - tipOffset.top - $tip.outerHeight(); + if (offsetBottom < 0) { + tipOffset.top = tipOffset.top + offsetBottom; + } + offsetRight = $('html').outerWidth() - tipOffset.left - $tip.outerWidth(); + if (offsetRight < 0) { + tipOffset.left = tipOffset.left + offsetRight; + } + if (tipOffset.top < 0) { + tipOffset.top = 0; + } + if (tipOffset.left < 0) { + tipOffset.left = 0; + } + $tip.offset(tipOffset); + if (step.placement === 'bottom' || step.placement === 'top') { + if (originalLeft !== tipOffset.left) { + return this._replaceArrow($tip, (tipOffset.left - originalLeft) * 2, offsetWidth, 'left'); + } + } else { + if (originalTop !== tipOffset.top) { + return this._replaceArrow($tip, (tipOffset.top - originalTop) * 2, offsetHeight, 'top'); + } + } + }; + + Tour.prototype._center = function($tip) { + return $tip.css('top', $(window).outerHeight() / 2 - $tip.outerHeight() / 2); + }; + + Tour.prototype._replaceArrow = function($tip, delta, dimension, position) { + return $tip.find('.arrow').css(position, delta ? 50 * (1 - delta / dimension) + '%' : ''); + }; + + Tour.prototype._scrollIntoView = function(element, callback) { + var $element, $window, counter, offsetTop, scrollTop, windowHeight; + $element = $(element); + if (!$element.length) { + return callback(); + } + $window = $(window); + offsetTop = $element.offset().top; + windowHeight = $window.height(); + scrollTop = Math.max(0, offsetTop - (windowHeight / 2)); + this._debug("Scroll into view. ScrollTop: " + scrollTop + ". Element offset: " + offsetTop + ". Window height: " + windowHeight + "."); + counter = 0; + return $('body, html').stop(true, true).animate({ + scrollTop: Math.ceil(scrollTop) + }, (function(_this) { + return function() { + if (++counter === 2) { + callback(); + return _this._debug("Scroll into view.\nAnimation end element offset: " + ($element.offset().top) + ".\nWindow height: " + ($window.height()) + "."); + } + }; + })(this)); + }; + + Tour.prototype._onResize = function(callback, timeout) { + return $(window).on("resize.tour-" + this._options.name, function() { + clearTimeout(timeout); + return timeout = setTimeout(callback, 100); + }); + }; + + Tour.prototype._initMouseNavigation = function() { + var _this; + _this = this; + return $(document).off("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='prev']").off("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='next']").off("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='end']").off("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='pause-resume']").on("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='next']", (function(_this) { + return function(e) { + e.preventDefault(); + return _this.next(); + }; + })(this)).on("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='prev']", (function(_this) { + return function(e) { + e.preventDefault(); + return _this.prev(); + }; + })(this)).on("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='end']", (function(_this) { + return function(e) { + e.preventDefault(); + return _this.end(); + }; + })(this)).on("click.tour-" + this._options.name, ".popover.tour-" + this._options.name + " *[data-role='pause-resume']", function(e) { + var $this; + e.preventDefault(); + $this = $(this); + $this.text(_this._paused ? $this.data('pause-text') : $this.data('resume-text')); + if (_this._paused) { + return _this.resume(); + } else { + return _this.pause(); + } + }); + }; + + Tour.prototype._initKeyboardNavigation = function() { + if (!this._options.keyboard) { + return; + } + return $(document).on("keyup.tour-" + this._options.name, (function(_this) { + return function(e) { + if (!e.which) { + return; + } + switch (e.which) { + case 39: + e.preventDefault(); + if (_this._isLast()) { + return _this.next(); + } else { + return _this.end(); + } + break; + case 37: + e.preventDefault(); + if (_this._current > 0) { + return _this.prev(); + } + break; + case 27: + e.preventDefault(); + return _this.end(); + } + }; + })(this)); + }; + + Tour.prototype._makePromise = function(result) { + if (result && $.isFunction(result.then)) { + return result; + } else { + return null; + } + }; + + Tour.prototype._callOnPromiseDone = function(promise, cb, arg) { + if (promise) { + return promise.then((function(_this) { + return function(e) { + return cb.call(_this, arg); + }; + })(this)); + } else { + return cb.call(this, arg); + } + }; + + Tour.prototype._showBackdrop = function(element) { + if (this.backdrop.backgroundShown) { + return; + } + this.backdrop = $('
', { + "class": 'tour-backdrop' + }); + this.backdrop.backgroundShown = true; + return $('body').append(this.backdrop); + }; + + Tour.prototype._hideBackdrop = function() { + this._hideOverlayElement(); + return this._hideBackground(); + }; + + Tour.prototype._hideBackground = function() { + if (this.backdrop) { + this.backdrop.remove(); + this.backdrop.overlay = null; + return this.backdrop.backgroundShown = false; + } + }; + + Tour.prototype._showOverlayElement = function(step) { + var $element, elementData; + $element = $(step.element); + if (!$element || $element.length === 0 || this.backdrop.overlayElementShown) { + return; + } + this.backdrop.overlayElementShown = true; + this.backdrop.$element = $element.addClass('tour-step-backdrop'); + this.backdrop.$background = $('
', { + "class": 'tour-step-background' + }); + elementData = { + width: $element.innerWidth(), + height: $element.innerHeight(), + offset: $element.offset() + }; + this.backdrop.$background.appendTo('body'); + if (step.backdropPadding) { + elementData = this._applyBackdropPadding(step.backdropPadding, elementData); + } + return this.backdrop.$background.width(elementData.width).height(elementData.height).offset(elementData.offset); + }; + + Tour.prototype._hideOverlayElement = function() { + if (!this.backdrop.overlayElementShown) { + return; + } + this.backdrop.$element.removeClass('tour-step-backdrop'); + this.backdrop.$background.remove(); + this.backdrop.$element = null; + this.backdrop.$background = null; + return this.backdrop.overlayElementShown = false; + }; + + Tour.prototype._applyBackdropPadding = function(padding, data) { + if (typeof padding === 'object') { + if (padding.top == null) { + padding.top = 0; + } + if (padding.right == null) { + padding.right = 0; + } + if (padding.bottom == null) { + padding.bottom = 0; + } + if (padding.left == null) { + padding.left = 0; + } + data.offset.top = data.offset.top - padding.top; + data.offset.left = data.offset.left - padding.left; + data.width = data.width + padding.left + padding.right; + data.height = data.height + padding.top + padding.bottom; + } else { + data.offset.top = data.offset.top - padding; + data.offset.left = data.offset.left - padding; + data.width = data.width + (padding * 2); + data.height = data.height + (padding * 2); + } + return data; + }; + + Tour.prototype._clearTimer = function() { + window.clearTimeout(this._timer); + this._timer = null; + return this._duration = null; + }; + + return Tour; + + })(); + return window.Tour = Tour; +})(jQuery, window); diff --git a/client/galaxy/scripts/mvc/tool/tool-form-composite.js b/client/galaxy/scripts/mvc/tool/tool-form-composite.js index 76b47a87611..3ca50acd22a 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-composite.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-composite.js @@ -332,4 +332,4 @@ define([ 'utils/utils', 'mvc/ui/ui-misc', 'mvc/form/form-view', 'mvc/form/form-d return { View: View }; -}); \ No newline at end of file +}); diff --git a/client/galaxy/scripts/mvc/tours.js b/client/galaxy/scripts/mvc/tours.js new file mode 100644 index 00000000000..32822e3ff77 --- /dev/null +++ b/client/galaxy/scripts/mvc/tours.js @@ -0,0 +1,62 @@ +/** + * This is the primary galaxy tours definition, currently only used for + * rendering a tour menu. + * + * For now it's intended to be plunked into the center display a-la + * Galaxy.app.display, but we could use a modal as well for more flexibility. + * + * DBTODO - This is downright backbone abuse, rewrite it. + */ + +define([],function() { + + var Tour = Backbone.Model.extend({ + urlRoot: '/api/tours', + }); + + var Tours = Backbone.Collection.extend({ + url: '/api/tours', + model: Tour, + }); + + var ToursView = Backbone.View.extend({ + // initialize + initialize: function(options) { + var self = this; + this.setElement('
'); + this.model = new Tours() + this.model.fetch({ + success: function( model ){ + console.log(model); + self.render(); + }, + error: function( model, response ){ + // Do something. + console.error("Failed to fetch tours."); + } + }); + }, + + render: function(){ + var tpl = _.template([ + "

Available Galaxy Tours

", + "
    ", + '<% _.each(tours, function(tour) { %>', + '
  • ', + '>', + '<%- tour.id %>', + '', + '- <%- tour.attributes.description %>', + '
    • ', + '<% }); %>', + "
"].join('')); + this.$el.html(tpl({tours: this.model.models, Galaxy: Galaxy})).on("click", ".tourItem", function(e){ + Galaxy.app.giveTour($(this).data("tour.id")); + }); + }, + + + }); + + return {ToursView: ToursView} +}); diff --git a/client/galaxy/scripts/mvc/upload/upload-button.js b/client/galaxy/scripts/mvc/upload/upload-button.js index 32cb194227f..3daf4fde670 100644 --- a/client/galaxy/scripts/mvc/upload/upload-button.js +++ b/client/galaxy/scripts/mvc/upload/upload-button.js @@ -77,7 +77,7 @@ var View = Backbone.View.extend({ return '
' + '
' + '
' + - '' + + '' + '' + '' + '
' + diff --git a/client/galaxy/style/less/galaxy_bootstrap/variables.less b/client/galaxy/style/less/galaxy_bootstrap/variables.less index 496ce0c2d65..2359b9719d0 100644 --- a/client/galaxy/style/less/galaxy_bootstrap/variables.less +++ b/client/galaxy/style/less/galaxy_bootstrap/variables.less @@ -267,7 +267,7 @@ @zindex-navbar: 1000; @zindex-dropdown: 1000; -@zindex-popover: 1010; +@zindex-popover: 1080; @zindex-tooltip: 1030; @zindex-navbar-fixed: 1030; @zindex-modal-background: 1040; diff --git a/client/grunt-tasks/install-libs.js b/client/grunt-tasks/install-libs.js index 9ac3ba604d9..529b45cf22c 100644 --- a/client/grunt-tasks/install-libs.js +++ b/client/grunt-tasks/install-libs.js @@ -23,6 +23,7 @@ module.exports = function( grunt ){ 'farbtastic': [ 'src/farbtastic.js', 'farbtastic.js' ], 'jQTouch': [ 'src/reference/jqtouch.js', 'jquery/jqtouch.js' ], + 'bootstrap-tour': [ 'build/js/bootstrap-tour.js', 'bootstrap-tour.js' ], // these need to be updated and tested //'jquery-form': [ 'jquery.form.js', 'jquery/jquery.form.js' ], @@ -90,4 +91,4 @@ module.exports = function( grunt ){ grunt.registerTask( 'copy-libs', 'copy external libraries to src', copyLibs ); grunt.registerTask( 'install-libs', 'fetch external libraries and copy to src', [ 'bower-install-simple:prod', 'copy-libs' ] ); -}; \ No newline at end of file +}; diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 0fde9285f67..eab93ed9bc3 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -249,6 +249,10 @@ paste.app_factory = galaxy.web.buildapp:app_factory # have security considerations, so proceed with caution. #interactive_environment_plugins_directory = +# Interactive tour directory: where to store interactive tour definition files. +# Set to config/plugins/tours to load the default tours that ship with Galaxy. +#tour_config_dir = + # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be # created. diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index d33446ac0e0..607118a83bc 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -14,6 +14,7 @@ from galaxy.visualization.genomes import Genomes from galaxy.visualization.data_providers.registry import DataProviderRegistry from galaxy.visualization.plugins.registry import VisualizationsRegistry from galaxy.tools.special_tools import load_lib_tools +from galaxy.tours import ToursRegistry from galaxy.sample_tracking import external_service_types from galaxy.openid.providers import OpenIDProviders from galaxy.tools.data_manager.manager import DataManagers @@ -105,6 +106,8 @@ class UniverseApplication( object, config.ConfiguresGalaxyMixin ): self, directories_setting=self.config.visualization_plugins_directory, template_cache_dir=self.config.template_cache ) + # Tours registry + self.tour_registry = ToursRegistry(self.config.tour_config_dir) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index e9f7e9af4b0..c351a544785 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -105,6 +105,8 @@ class Configuration( object ): self.user_label_filters = listify( kwargs.get( "user_tool_label_filters", [] ), do_strip=True ) self.user_section_filters = listify( kwargs.get( "user_tool_section_filters", [] ), do_strip=True ) + self.tour_config_dir = resolve_path( kwargs.get("tour_config_dir", ""), self.root) + self.expose_user_name = kwargs.get( "expose_user_name", False ) self.expose_user_email = kwargs.get( "expose_user_email", False ) diff --git a/lib/galaxy/tours/__init__.py b/lib/galaxy/tours/__init__.py new file mode 100644 index 00000000000..fccc06fbbe4 --- /dev/null +++ b/lib/galaxy/tours/__init__.py @@ -0,0 +1,59 @@ +""" +This module manages loading/etc of Galaxy interactive tours. +""" + +import os +import yaml +import logging +log = logging.getLogger( __name__ ) + + +def tour_loader(contents_dict): + # This *COULD* be done on the clientside. Maybe even should? + for step in contents_dict['steps']: + if 'intro' in step: + step['content'] = step.pop('intro') + if 'position' in step: + step['placement'] = step.pop('position') + # Handle these hooks on the client side, instead of trying to ship + # functions as strings and eval + # if 'preclick' in step: + # step['onShow'] = "$('%s').click()" % step.pop('preclick') + # if 'postclick' in step: + # step['onHide'] = "$('%s').click()" % step.pop('postclick') + # if 'textinsert' in step: + # step['onShown'] = "$('%s').text('%s')" % (step['element'], step.pop('textinsert')) + if 'element' not in step: + step['orphan'] = True + return contents_dict + + +class ToursRegistry(object): + + def __init__(self, tour_dir): + self.tour_dir = tour_dir + self.load_tours() + + def tours_by_id_with_description(self): + return [{'id': k, + 'description': self.tours[k].get('description', None)} + for k in self.tours.keys()] + + def load_tours(self): + self.tours = {} + for f in os.listdir(self.tour_dir): + if f.endswith('.yaml'): + tour_path = os.path.join(self.tour_dir, f) + with open(tour_path) as handle: + conf = yaml.load(handle) + # Could pop the following, but is there a good reason to? + # As long as they key doesn't conflict with tour keys, it's + # fine. + tour_id = conf.get('tour_id', f.strip('.yaml')) + self.tours[tour_id] = tour_loader(conf) + log.info("Loaded tour '%s'" % tour_id) + + def tour_contents(self, tour_id): + # Extra format translation could happen here (like the previous intro_to_tour) + # For now just return the loaded contents. + return self.tours.get(tour_id, None) diff --git a/lib/galaxy/webapps/galaxy/api/tours.py b/lib/galaxy/webapps/galaxy/api/tours.py new file mode 100644 index 00000000000..4905b7de46b --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/tours.py @@ -0,0 +1,34 @@ +""" +API Controller providing Galaxy Tours +""" +import logging +from galaxy.web import _future_expose_api_anonymous_and_sessionless as expose_api_anonymous_and_sessionless +from galaxy.web.base.controller import BaseAPIController + +log = logging.getLogger( __name__ ) + + +class ToursController( BaseAPIController ): + + def __init__( self, app ): + super( ToursController, self ).__init__( app ) + + @expose_api_anonymous_and_sessionless + def index( self, trans, **kwd ): + """ + *GET /api/tours/ + Displays available tours + """ + return trans.app.tour_registry.tours_by_id_with_description() + + @expose_api_anonymous_and_sessionless + def show( self, trans, tour_id, **kwd ): + """ + load_config( self, trans, Tour_config_file, **kwd ) + * GET /api/tours/{tour_config_file}: + Read a yaml file containing the specified tour definition + + :returns: tour definition + :rtype: dictionary + """ + return trans.app.tour_registry.tour_contents(tour_id) diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index 7895d1da5d7..4452f4e0cc1 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -393,6 +393,22 @@ def populate_api_routes( webapp, app ): action='get_api_key', conditions=dict( method=[ "GET" ] ) ) + # ===================== + # ===== TOURS API ===== + # ===================== + + webapp.mapper.connect( 'index', + '/api/tours', + controller='tours', + action='index', + conditions=dict( method=["GET"] ) ) + + webapp.mapper.connect( 'show', + '/api/tours/{tour_id}', + controller='tours', + action='show', + conditions=dict( method=[ "GET" ] ) ) + # ======================= # ===== LIBRARY API ===== # ======================= diff --git a/static/maps/galaxy.menu.js.map b/static/maps/galaxy.menu.js.map new file mode 100644 index 00000000000..5979b2873a0 --- /dev/null +++ b/static/maps/galaxy.menu.js.map @@ -0,0 +1 @@ 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    ","<% } %>"]),deleted:i.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',n("This collection has been deleted"),"
    ","<% } %>"])}),e=i.wrapTemplate(['
    ','
    ','<%- collection.element_identifier || collection.name %>',"
    ",'
    ',"
    "],"collection");return o.extend({},s.prototype.templates,{warnings:t,titleBar:e})}();var d=l.extend({className:l.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DCEListItemView.initialize:",t),l.prototype.initialize.call(this,t)},toString:function(){var t=this.model?this.model+"":"(no model)";return"DCEListItemView("+t+")"}});d.prototype.templates=function(){var t=i.wrapTemplate(['
    ','
    ','<%- element.element_identifier %>',"
    ",'
    ',"
    "],"element");return o.extend({},l.prototype.templates,{titleBar:t})}();var h=e.DatasetListItemView.extend({className:e.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log("DatasetDCEListItemView.initialize:",t),e.DatasetListItemView.prototype.initialize.call(this,t)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):r.when()},toString:function(){var t=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+t+")"}});h.prototype.templates=function(){var t=i.wrapTemplate(['
    ','','
    ','<%- element.element_identifier %>',"
    ","
    "],"element");return o.extend({},e.DatasetListItemView.prototype.templates,{titleBar:t})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(t){c.prototype._swapNewRender.call(this,t);var e=this.model.get("state")||"ok";return this.$el.addClass("state-"+e),this.$el},toString:function(){var t=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+t+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(94),i(6),i(5)],s=function(t,e,i){var n="collections",s={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(t){return o.extend(t,t.object,{element_id:t.id}),delete t.object,t},constructor:function(t,e){t=this._mergeObject(t),this.idAttribute="element_id",a.Model.apply(this,arguments)},parse:function(t,e){var i=t;return i=this._mergeObject(i)}},l=a.Model.extend(e.LoggableMixin).extend(s).extend({_logNamespace:n}),c=a.Collection.extend(e.LoggableMixin).extend({_logNamespace:n,model:l,initialize:function(t,e){this.debug(this+"(DCECollection).initialize:",t,e),e=e||{}},toString:function(){return["DatasetCollectionElementCollection(",this.length,")"].join("")}}),d=t.DatasetAssociation.extend(e.mixin(s,{url:function(){return this.has("history_id")?Galaxy.root+"api/histories/"+this.get("history_id")+"/contents/"+this.get("id"):(console.warn("no endpoint for non-hdas within a collection yet"),Galaxy.root+"api/datasets")},defaults:o.extend({},t.DatasetAssociation.prototype.defaults,s.defaults),constructor:function(t,e){this.debug(" DatasetDCE.constructor:",t,e),s.constructor.call(this,t,e)},initialize:function(e,i){this.debug(this+"(DatasetDCE).initialize:",e,i),t.DatasetAssociation.prototype.initialize.call(this,e,i)},hasDetails:function(){return o.has(this.attributes,"annotation")},toString:function(){var t=this.get("element_identifier");return["DatasetDCE(",t,")"].join("")}})),h=c.extend({model:d,initialize:function(t,e){this.debug(this+"(DatasetDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),u=a.Model.extend(e.LoggableMixin).extend(e.SearchableModelMixin).extend({_logNamespace:n,defaults:{collection_type:null,deleted:!1},collectionClass:c,initialize:function(t,e){this.debug(this+"(DatasetCollection).initialize:",t,e,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var t=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(t),this.elements},toJSON:function(){var t=a.Model.prototype.toJSON.call(this);return this.elements&&(t.elements=this.elements.toJSON()),t},inReadyState:function(){var t=this.get("populated");return this.isDeletedOrPurged()||t},hasDetails:function(){return this.debug("hasDetails:",this.elements.length),0!==this.elements.length},getVisibleContents:function(t){return this.elements},"delete":function(t){return this.get("deleted")?r.when():this.save({deleted:!0},t)},undelete:function(t){return!this.get("deleted")||this.get("purged")?r.when():this.save({deleted:!1},t)},isDeletedOrPurged:function(){return this.get("deleted")||this.get("purged")},searchAttributes:["name"],toString:function(){var t=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+t.join(",")+")"}}),p=u.extend({collectionClass:h,initialize:function(t,e){this.debug(this+"(ListDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListDatasetCollection(",this.get("name"),")"].join("")}}),f=p.extend({initialize:function(t,e){this.debug(this+"(PairDatasetCollection).initialize:",t,e),p.prototype.initialize.call(this,t,e)},toString:function(){return["PairDatasetCollection(",this.get("name"),")"].join("")}}),g=u.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",t,")"].join("")}})),m=c.extend({model:g,initialize:function(t,e){this.debug(this+"(NestedDCDCECollection).initialize:",t,e),c.prototype.initialize.call(this,t,e)},toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),v=f.extend(e.mixin(s,{constructor:function(t,e){this.debug(" NestedPairDCDCE.constructor:",t,e),s.constructor.call(this,t,e)},toString:function(){var t=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",t,")"].join("")}})),_=m.extend({model:v,initialize:function(t,e){this.debug(this+"(NestedPairDCDCECollection).initialize:",t,e),m.prototype.initialize.call(this,t,e)},toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),y=u.extend({collectionClass:_,initialize:function(t,e){this.debug(this+"(ListPairedDatasetCollection).initialize:",t,e),u.prototype.initialize.call(this,t,e)},toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:p,PairDatasetCollection:f,ListPairedDatasetCollection:y}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3),i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(45),i(15),i(6),i(10),i(108),i(5),i(105)],s=function(t,e,i,n,s,c){function d(t){var e=t.toJSON(),i=g(e,{creationFn:function(e,i){return e=e.map(function(t){return{id:t.id,name:t.name,src:"dataset"===t.history_content_type?"hda":"hdca"}}),t.createHDCA(e,"list",i)}});return i}var h="collections",u=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,tagName:"li",className:"collection-element",initialize:function(t){this.element=t.element||{},this.selected=t.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name %>","",'"].join("")),select:function(t){this.$el.toggleClass("selected",t),this.trigger("select",{source:this,selected:this.$el.hasClass("selected")})},discard:function(){var t=this,e=this.$el.parent().width();this.$el.animate({"margin-right":e},"fast",function(){t.trigger("discard",{source:t}),t.destroy()})},destroy:function(){this.off(),this.$el.remove()},events:{click:"_click","click .name":"_clickName","click .discard":"_clickDiscard",dragstart:"_dragstart",dragend:"_dragend",dragover:"_sendToParent",drop:"_sendToParent"},_click:function(t){t.stopPropagation(),this.select(t)},_clickName:function(t){t.stopPropagation(),t.preventDefault();var e=([c("Enter a new name for the element"),":\n(",c("Note that changing the name here will not rename the dataset"),")"].join(""),prompt(c("Enter a new name for the element")+":",this.element.name));e&&(this.element.name=e,this.render())},_clickDiscard:function(t){t.stopPropagation(),this.discard()},_dragstart:function(t){t.originalEvent&&(t=t.originalEvent),t.dataTransfer.effectAllowed="move",t.dataTransfer.setData("text/plain",JSON.stringify(this.element)),this.$el.addClass("dragging"),this.$el.parent().trigger("collection-element.dragstart",[this])},_dragend:function(t){this.$el.removeClass("dragging"),this.$el.parent().trigger("collection-element.dragend",[this])},_sendToParent:function(t){this.$el.parent().trigger(t)},toString:function(){return"DatasetCollectionElementView()"}}),p=o.View.extend(i.LoggableMixin).extend({_logNamespace:h,elementViewClass:u,collectionClass:t.HistoryListDatasetCollection,className:"list-collection-creator collection-creator flex-row-container",minElements:1,defaultAttributes:{creationFn:function(){throw new TypeError("no creation fn for creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},initialize:function(t){this.metric("ListCollectionCreator.initialize",t);var e=this;a.each(this.defaultAttributes,function(i,n){i=t[n]||i,e[n]=i}),e.initialElements=t.elements||[],this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(t){t.hasOwnProperty("id")||(t.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var t=this;return t.invalidElements=[],this.workingElements=this.workingElements.filter(function(e){var i=t._isElementInvalid(e);return i&&t.invalidElements.push({element:e,text:i}),!i}),this.workingElements},_isElementInvalid:function(t){return"dataset"!==t.history_content_type?c("is not a dataset"):t.state!==e.OK?c(a.contains(e.NOT_READY_STATES,t.state)?"hasn't finished running yet":"has errored, is paused, or is not accessible"):t.deleted||t.purged?c("has been deleted or purged"):null},_mangleDuplicateNames:function(){var t=900,e=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+e+")",e+=1,e>=t)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(t){},render:function(t,e){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(t,e){var i=this,n=l("
    "),s=i.$list();a.each(this.elementViews,function(t){t.destroy(),i.removeElementView(t)}),i.workingElements.forEach(function(t){var e=i._createElementView(t);n.append(e.$el)}),i._renderClearSelected(),s.empty().append(n.children()),a.invoke(i.elementViews,"render"),s.height()>s.css("max-height")?s.css("border-width","1px 0px 1px 0px"):s.css("border-width","0px")},_createElementView:function(t){var e=new this.elementViewClass({element:t,selected:a.has(this.selectedIds,t.id)});return this.elementViews.push(e),this._listenToElementView(e),e},_listenToElementView:function(t){var e=this;e.listenTo(t,{select:function(t){var i=t.source.element;t.selected?e.selectedIds[i.id]=!0:delete e.selectedIds[i.id],e.trigger("elements:select",t)},discard:function(t){e.trigger("elements:discard",t)}})},addElementView:function(t){},removeElementView:function(t){delete this.selectedIds[t.element.id],this._renderClearSelected(),this.elementViews=a.without(this.elementViews,t),this.stopListening(t)},_renderNoElementsLeft:function(){this._disableNameAndCreate(!0),this.$(".collection-elements").append(this.templates.noElementsLeft())},_elementToJSON:function(t){return t},createList:function(t){if(!this.workingElements.length){var e=c("No valid elements for final list")+". ";return e+=''+c("Cancel")+" ",e+=c("or"),e+=' '+c("start over")+".",void this._showAlert(e)}var i=this,n=this.workingElements.map(function(t){return i._elementToJSON(t)});return i.blocking=!0,i.creationFn(n,t).always(function(){i.blocking=!1}).fail(function(t,e,n){i.trigger("error",{xhr:t,status:e,message:c("An error occurred while creating this collection")})}).done(function(t,e,n){i.trigger("collection:created",t,e,n),i.metric("collection:created",t),"function"==typeof i.oncreate&&i.oncreate.call(this,t,e,n)})},_setUpBehaviors:function(){return this.on("error",this._errorHandler),this.once("rendered",function(){this.trigger("rendered:initial",this)}),this.on("elements:select",function(t){this._renderClearSelected()}),this.on("elements:discard",function(t){var e=t.source.element;this.removeElementView(t.source),this.workingElements=a.without(this.workingElements,e),this.workingElements.length||this._renderNoElementsLeft()}),this},_errorHandler:function(t){this.error(t);var e=this;if(content=t.message||c("An error occurred"),t.xhr){var i=t.xhr,n=t.message;0===i.readyState&&0===i.status?content+=": "+c("Galaxy could not be reached and may be updating.")+c(" Try again in a few minutes."):i.responseJSON?content+=":
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    ":content+=": "+n}e._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","click .cancel-create":function(t){"function"==typeof this.oncancel&&this.oncancel.call(this)},"click .create-collection":"_clickCreate"},_clickMoreHelp:function(t){t.stopPropagation(),this.$(".main-help").addClass("expanded"),this.$(".more-help").hide()},_clickLessHelp:function(t){t.stopPropagation(),this.$(".main-help").removeClass("expanded"),this.$(".more-help").show()},_toggleHelp:function(t){t.stopPropagation(),this.$(".main-help").toggleClass("expanded"),this.$(".more-help").toggle()},_showAlert:function(t,e){e=e||"alert-danger",this.$(".main-help").hide(),this.$(".header .alert").attr("class","alert alert-dismissable").addClass(e).show().find(".alert-message").html(t)},_hideAlert:function(t){this.$(".main-help").show(),this.$(".header .alert").hide()},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(t){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(t){t.preventDefault();var e=this.$list();this._checkForAutoscroll(e,t.originalEvent.clientY);var i=this._getNearestElement(t.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=r('
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    ','
    ','
    '].join("")),header:a.template(['
    ','',c("More help"),"",'
    ','',c("Less"),"","
    ","
    ",'
    ','','',"
    "].join("")),middle:a.template(['
    ','',c("Start over"),"",'',c("Clear selected"),"","
    ",'
    ',"
    "].join("")),footer:a.template(['
    ','
    ','','
    ',c("Name"),":
    ","
    ","
    ",'
    ','
    ','",'
    ','",'","
    ","
    ",'
    ','","
    ","
    "].join("")),helpContent:a.template(["

    ",c(["Collections of datasets are permanent, ordered lists of datasets that can be passed to tools and ","workflows in order to have analyses done on each member of the entire group. This interface allows ","you to create a collection and re-order the final collection."].join("")),"

    ","
      ","
    • ",c(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
      • ","
    • ",c(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
      • ","
    • ",c(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
      • ","
    • ",c(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
      • ","
    • ",c(['Click the "Cancel" button to exit the interface.'].join("")),"
      • ","

    ","

    ",c(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

    "].join("")),invalidElements:a.template([c("The following selections could not be included due to problems:"),"
      <% _.each( problems, function( problem ){ %>","
    • <%- problem.element.name %>: <%- problem.text %>
      • ","<% }); %>
    "].join("")),noElementsLeft:a.template(['
  • ',c("No elements left! "),c("Would you like to "),'',c("start over"),"?","
    • "].join("")),invalidInitial:a.template(['
    ','
    ','',"<% if( _.size( problems ) ){ %>",c("The following selections could not be included due to problems"),":","
      <% _.each( problems, function( problem ){ %>","
    • <%- problem.element.name %>: <%- problem.text %>
      • ","<% }); %>
    ","<% } else if( _.size( elements ) < 1 ){ %>",c("No datasets were selected"),".","<% } %>","
    ",c("At least one element is needed for the collection"),". ",c("You may need to "),'',c("cancel")," ",c("and reselect new elements"),".","    ","
    ","
    ",'
    ','
    ','
    ','","
    ","
    ","
    "].join(""))},toString:function(){return"ListCollectionCreator"}}),f=function(t,e,i){var s,o=l.Deferred(),r=Galaxy.modal||new n.View;return e=a.defaults(e||{},{elements:t,oncancel:function(){r.hide(),o.reject("cancelled")},oncreate:function(t,e){r.hide(),o.resolve(e)}}),s=new i(e),r.show({title:e.title||c("Create a collection"),body:s.$el,width:"80%",height:"min-content",closing_events:!0}),s.render(),window._collectionCreator=s,o},g=function(t,e){return e=e||{},e.title=c("Create a collection from a list of datasets"),f(t,e,p)};return{DatasetCollectionElementView:u,ListCollectionCreator:p,collectionCreatorModal:f,listCollectionCreatorModal:g,createListCollection:d}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(48),i(15),i(26),i(6),i(5)],s=function(t,e,i,n,s){var c="dataset",d=t.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(t){t.logger&&(this.logger=this.model.logger=t.logger),this.log(this+".initialize:",t),d.prototype.initialize.call(this,t),this.linkTarget=t.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this), this.model.on("change",function(t,e){this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()?this.model.fetch():this.render()},this)},_fetchModelDetails:function(){var t=this;return t.model.inReadyState()&&!t.model.hasDetails()?t.model.fetch({silent:!0}):o.when()},remove:function(t,e){var i=this;t=t||this.fxSpeed,this.$el.fadeOut(t,function(){a.View.prototype.remove.call(i),e&&e.call(i)})},render:function(t){return d.prototype.render.call(this,t)},_swapNewRender:function(t){return d.prototype._swapNewRender.call(this,t),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var t=this.model.get("state");if(t===e.NOT_VIEWABLE||t===e.DISCARDED||!this.model.get("accessible"))return null;var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(t===e.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(t===e.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(t){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add_dataset(o.model.get("id")),t.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===e.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var t=d.prototype._renderDetails.call(this);return t.find(".actions .left").empty().append(this._renderSecondaryActions()),t.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),t.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(t),t},_renderSummary:function(){var t=this.model.toJSON(),e=this.templates.summaries[t.state];return(e=e||this.templates.summaries.unknown)(t,this)},_renderDetailMessages:function(){var t=this,e=r('
    '),i=t.model.toJSON();return l.each(t.templates.detailMessages,function(n){e.append(r(n(i,t)))}),e},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case e.NOT_VIEWABLE:return[];case e.OK:case e.FAILED_METADATA:case e.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:l.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var t=this.model.urls;return r(['
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    ","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'
    ',s("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'
    ',s("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',s("This dataset has been deleted"),"
    ","<% } %>"])}),i=n.wrapTemplate(['
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    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
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    ',"<% } %>","<% } %>","
    "],"dataset"),o=n.wrapTemplate(['
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    ',s("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),a={};a[e.OK]=a[e.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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    ","<% } %>","<% if( dataset.file_ext ){ %>",'
    ','",'<%- dataset.file_ext %>',"
    ","<% } %>","<% if( dataset.metadata_dbkey ){ %>",'
    ','",'',"<%- dataset.metadata_dbkey %>","","
    ","<% } %>","<% if( dataset.misc_info ){ %>",'
    ','<%- dataset.misc_info %>',"
    ","<% } %>"],"dataset"),a[e.NEW]=n.wrapTemplate(["
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    "],"dataset"),a[e.NOT_VIEWABLE]=n.wrapTemplate(["
    ",s("You do not have permission to view this dataset"),"
    "],"dataset"),a[e.DISCARDED]=n.wrapTemplate(["
    ",s("The job creating this dataset was cancelled before completion"),"
    "],"dataset"),a[e.QUEUED]=n.wrapTemplate(["
    ",s("This job is waiting to run"),"
    "],"dataset"),a[e.RUNNING]=n.wrapTemplate(["
    ",s("This job is currently running"),"
    "],"dataset"),a[e.UPLOAD]=n.wrapTemplate(["
    ",s("This dataset is currently uploading"),"
    "],"dataset"),a[e.SETTING_METADATA]=n.wrapTemplate(["
    ",s("Metadata is being auto-detected"),"
    "],"dataset"),a[e.PAUSED]=n.wrapTemplate(["
    ",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
    "],"dataset"),a[e.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","
    <%- dataset.misc_blurb %>
    ","<% } %>",'',s("An error occurred with this dataset"),":",'
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    '],"dataset"),a[e.EMPTY]=n.wrapTemplate(["
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    "],"dataset"),a.unknown=n.wrapTemplate(['
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    '],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'
    ',s("The job creating this dataset has been resubmitted"),"
    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
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    ","<% }); %>"],"apps");return l.extend({},d.prototype.templates,{warnings:t,details:i,noAccess:o,summaries:a,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1),i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4)],s=function(t){var e=o.Model.extend({initialize:function(t){this.app=t},checksum:function(){var t="",e=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=e.app.field_list[i];n&&(t+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),t},create:function(){function t(t,e,i){n.flat_dict[t]=e,o[t]=i}function e(s,o){for(var a in o){var r=o[a];if(r.input){var l=r.input,c=s;switch(""!=s&&(c+="|"),c+=l.name,l.type){case"repeat":var d="section-",h=[],u=null;for(var p in r){var f=p.indexOf(d);-1!=f&&(f+=d.length,h.push(parseInt(p.substr(f))),u||(u=p.substr(0,f)))}h.sort(function(t,e){return t-e});var a=0;for(var g in h)e(c+"_"+a++,r[u+h[g]]);break;case"conditional":var m=n.app.field_list[l.id].value();t(c+"|"+l.test_param.name,l.id,m);var v=i(l,m);-1!=v&&e(c,o[l.id+"-section-"+v]);break;case"section":e(!l.flat&&c||"",r);break;default:var _=n.app.field_list[l.id];if(_&&_.value){var m=_.value();if((void 0===l.ignore||l.ignore!=m)&&(_.collapsed&&l.collapsible_value&&(m=l.collapsible_value),t(c,l.id,m),l.payload))for(var y in l.payload)t(y,l.id,l.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},e("",s),o},match:function(t){return this.flat_dict&&this.flat_dict[t]},matchCase:function(t,e){return i(t,e)},matchModel:function(t,e){return s(t.inputs,this.flat_dict,e)},matchResponse:function(t){function e(t,s){if("string"==typeof s){var o=n.flat_dict[t];o&&(i[o]=s)}else for(var a in s){var r=a;if(""!==t){var l="|";s instanceof Array&&(l="_"),r=t+l+r}e(r,s[a])}}var i={},n=this;return e("",t),i},_iterate:function(t,e){var i=this,n=a(t).children();n.each(function(){var t=this,n=a(t).attr("id");if(a(t).hasClass("section-row")){var s=i.app.input_list[n];e[n]=s&&{input:s}||{},i._iterate(t,e[n])}else i._iterate(t,e)})}}),i=function(t,e){"boolean"==t.test_param.type&&(e="true"==e?t.test_param.truevalue||"true":t.test_param.falsevalue||"false");for(var i in t.cases)if(t.cases[i].value==e)return i;return-1},n=function(t,e,i,s){s=a.extend(!0,{},s),r.each(t,function(t){t&&t.type&&(s[t.name]=t)}),r.each(t,function(t){r.isObject(t)&&(t.type&&s[t[e]]?i(t,s[t[e]]):n(t,e,i,s))})},s=function(t,e,n){function s(t,o){for(var a in o){var r=o[a],l=r.name;switch(""!=t&&(l=t+"|"+l),r.type){case"repeat":for(var c in r.cache)s(l+"_"+c,r.cache[c]);break;case"conditional":var d=i(r,r.test_param&&r.test_param.value);-1!=d&&s(l,r.cases[d].inputs);break;case"section":s(l,r.inputs);break;default:var h=e[l];h&&n(h,r)}}}var o={};return s("",t),o};return{Manager:e,matchIds:s,matchContext:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(i){n=[],s=function(){return i.View.extend({initialize:function(t,e){this.app=t,this.field=e.field,this.text_enable=t.options.text_enable||"Enable",this.text_disable=t.options.text_disable||"Disable",this.cls_enable=t.options.cls_enable||"fa fa-caret-square-o-down",this.cls_disable=t.options.cls_disable||"fa fa-caret-square-o-up",this.setElement(this._template(e)),this.$field=this.$(".ui-form-field"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_icon=this.$(".ui-form-collapsible").find(".icon"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el),this.field.collapsed=void 0!==e.collapsible_value&&JSON.stringify(e.value)==JSON.stringify(e.collapsible_value),this._refresh();var i=this;this.$collapsible.on("click",function(){i.field.collapsed=!i.field.collapsed,i._refresh()})},disable:function(t){this.$backdrop.show(),t&&this.$backdrop.css({opacity:0,cursor:"default"})},error:function(t){this.$error_text.html(t),this.$error.show(),this.$el.addClass("ui-error")},reset:function(){this.$error.hide(),this.$el.removeClass("ui-error")},_refresh:function(){this.$collapsible_icon.removeClass().addClass("icon"),this.field.collapsed?(this.$field.hide(),this.$preview.show(),this._tooltip(this.text_enable,this.cls_enable)):(this.$field.fadeIn("fast"),this.$preview.hide(),this._tooltip(this.text_disable,this.cls_disable)),this.app.trigger("change")},_tooltip:function(t,e){this.$collapsible_icon.addClass(e).tooltip({placement:"bottom"}).attr("data-original-title",t).tooltip("fixTitle").tooltip("hide")},_template:function(t){var e='
    ';return e+=t.disabled||void 0===t.collapsible_value?t.label:'
    '+t.label+"
    ",e+='
    ',e+='
    ',t.help&&(e+=t.help,t.argument&&-1==t.help.indexOf("("+t.argument+")")&&(e+=" ("+t.argument+")")),e+='
    ',t.collapsible_preview&&(e+='
    '+t.text_value+"
    "),e+="
    "}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2))},function(t,e,i){var n,s;(function(o,a){n=[i(4),i(7),i(43),i(56),i(55),i(52)],s=function(t,e,i,n,s,r){return o.Model.extend({types:{text:"_fieldText",select:"_fieldSelect",data_column:"_fieldSelect",genomebuild:"_fieldSelect",data:"_fieldData",data_collection:"_fieldData",integer:"_fieldSlider","float":"_fieldSlider","boolean":"_fieldBoolean",drill_down:"_fieldDrilldown",color:"_fieldColor",hidden:"_fieldHidden",hidden_data:"_fieldHidden",baseurl:"_fieldHidden",library_data:"_fieldLibrary",ftpfile:"_fieldFtp"},initialize:function(t,e){this.app=t},create:function(t){void 0===t.value&&(t.value=null),void 0===t.default_value&&(t.default_value=t.value);var e=null,i=this.types[t.type];return i&&"function"==typeof this[i]&&(e=this[i].call(this,t)),e||(this.app.incompatible=!0,e=t.options?this._fieldSelect(t):this._fieldText(t),Galaxy.emit.debug("form-parameters::_addRow()","Auto matched field type ("+t.type+").")),void 0!==t.value&&e.value(t.value),e},_fieldData:function(t){var e=this;return new i.View(this.app,{id:"field-"+t.id,extensions:t.extensions,optional:t.optional,multiple:t.multiple,type:t.type,data:t.options,onchange:function(){e.app.trigger("change")}})},_fieldSelect:function(t){if(t.is_workflow)return this._fieldText(t);"data_column"==t.type&&(t.error_text="Missing columns in referenced dataset.");var i=[];for(var n in t.options){var s=t.options[n];i.push({label:s[0],value:s[1]})}var o=e.Select;switch(t.display){case"checkboxes":o=e.Checkbox;break;case"radio":o=e.Radio}var a=this;return new o.View({id:"field-"+t.id,data:i,error_text:t.error_text||"No options available",optional:t.optional&&null===t.default_value,multiple:t.multiple,optional:t.optional,searchable:t.searchable,onchange:function(){a.app.trigger("change")}})},_fieldDrilldown:function(t){if(t.is_workflow)return this._fieldText(t);var i=this;return new e.Drilldown.View({id:"field-"+t.id,data:t.options,display:t.display,onchange:function(){i.app.trigger("change")}})},_fieldText:function(i){if(i.options)if(i.area=i.multiple,t.validate(i.value)){if(a.isArray(i.value)){var n="";for(var s in i.value){if(n+=String(i.value[s]),!i.multiple)break;n+="\n"}i.value=n}}else i.value=null;var o=this;return new e.Input({id:"field-"+i.id,area:i.area,onchange:function(){o.app.trigger("change")}})},_fieldSlider:function(t){var i=this;return new e.Slider.View({id:"field-"+t.id,precise:"float"==t.type,is_workflow:t.is_workflow,min:t.min,max:t.max,onchange:function(){i.app.trigger("change")}})},_fieldHidden:function(t){return new e.Hidden({id:"field-"+t.id,info:t.info})},_fieldBoolean:function(t){var i=this;return new e.RadioButton.View({id:"field-"+t.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){i.app.trigger("change")}})},_fieldColor:function(t){var e=this;return new r({id:"field-"+t.id,onchange:function(){e.app.trigger("change")}})},_fieldLibrary:function(t){var e=this;return new n.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})},_fieldFtp:function(t){var e=this;return new s.View({id:"field-"+t.id,optional:t.optional,multiple:t.multiple,onchange:function(){e.app.trigger("change")}})}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(17),i(11),i(7)],s=function(t,e,i,n){var s=o.View.extend({initialize:function(i){this.options=t.merge(i,{title:"Section",empty_text:"Not available.",max:null,min:null}),this.setElement("
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    ").append(this.button_new.$el)),this.list={},this.n=0},size:function(){return this.n},add:function(t){if(!t.id||this.list[t.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate repeat block id.");this.n++;var e=new n.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain",onclick:function(){t.ondel&&t.ondel()}}),s=new i.View({id:t.id,title:"placeholder",cls:"ui-portlet-repeat",operations:{button_delete:e}});s.append(t.$el),s.$el.addClass("section-row"),this.list[t.id]=s,this.table.add(s.$el),this.table.append("row_"+t.id,!0),this.options.max>0&&this.n>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(t){if(!this.list[t])return void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.");this.n--;var e=this.table.get("row_"+t);e.remove(),delete this.list[t],this.button_new.enable(),this._refresh()},hideOptions:function(){this.button_new.$el.hide(),r.each(this.list,function(t){t.hideOperation("button_delete")}),r.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var t=0;for(var e in this.list){var i=this.list[e];i.title(++t+": "+this.options.title),this.n>this.options.min?i.showOperation("button_delete"):i.hideOperation("button_delete")}}});return{View:s}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(4),i(17),i(7),i(11),i(41),i(39),i(40)],s=function(t,e,i,n,s,c,d){var h=o.View.extend({initialize:function(t,i){this.app=t,this.inputs=i.inputs,i.cls="ui-table-plain",i.cls_tr="section-row",this.table=new e.View(i),this.parameters=new d(t,i),this.setElement(this.table.$el),this.render()},render:function(){this.table.delAll();for(var t in this.inputs)this.add(this.inputs[t])},add:function(e){var i=a.extend(!0,{},e);i.id=e.id=t.uid(),this.app.input_list[i.id]=i;var n=i.type;switch(n){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(t){var e=this;t.test_param.id=t.id,this.app.options.sustain_conditionals&&(t.test_param.disabled=!0);var i=this._addRow(t.test_param);i.options.onchange=function(i){var n=e.app.data.matchCase(t,i);for(var s in t.cases){var o=t.cases[s],a=t.id+"-section-"+s,r=e.table.get(a),l=!1;for(var c in o.inputs)if(!o.inputs[c].hidden){l=!0;break}s==n&&l?r.fadeIn("fast"):r.hide()}e.app.trigger("change")};for(var n in t.cases){var s=t.id+"-section-"+n,o=new h(this.app,{inputs:t.cases[n].inputs});o.$el.addClass("ui-table-section"),this.table.add(o.$el),this.table.append(s)}i.trigger("change")},_addRepeat:function(t){function e(e){var s=t.id+"-section-"+n++,a=new h(i.app,{inputs:e});o.add({id:s,$el:a.$el,ondel:function(){o.del(s),i.app.trigger("change")}})}for(var i=this,n=0,o=new s.View({title:t.title||"Repeat",title_new:t.title||"",min:t.min,max:t.max,onnew:function(){e(t.inputs),i.app.trigger("change")}}),a=t.min,l=r.size(t.cache),d=0;dd?t.cache[d]:t.inputs,e(u)}this.app.options.sustain_repeats&&o.hideOptions();var p=new c(this.app,{label:t.title||t.name,help:t.help,field:o});this.table.add(p.$el),this.table.append(t.id)},_addSection:function(t){var e=this,s=new h(e.app,{inputs:t.inputs}),o=new i.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"}),a=new n.View({title:t.title||t.name,cls:"ui-portlet-section",collapsible:!0,collapsed:!0,operations:{button_visible:o}});a.append(s.$el),a.append(l("
    ").addClass("ui-form-info").html(t.help)),a.setOperation("button_visible",function(){a.collapsed?a.expand():a.collapse()}),a.on("expanded",function(){o.setIcon("fa-eye")}),a.on("collapsed",function(){o.setIcon("fa-eye-slash")}),this.app.on("expand",function(t){a.$("#"+t).length>0&&a.expand()}),t.expanded&&a.expand(),this.table.add(a.$el),this.table.append(t.id)},_addRow:function(t){var e=t.id,i=this.parameters.create(t);this.app.field_list[e]=i;var n=new c(this.app,{name:t.name,label:t.label||t.name,value:t.value,default_value:t.default_value,text_value:t.text_value||t.value,collapsible_value:t.collapsible_value,collapsible_preview:t.collapsible_preview,help:t.help,argument:t.argument,disabled:t.disabled,field:i});return this.app.element_list[e]=n,this.table.add(n.$el),this.table.append(e),t.hidden&&this.table.get(e).hide(),i}});return{View:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(7),i(31)],s=function(t,e,i){var n=o.View.extend({initialize:function(i,n){this.app=i,this.options=n,this.history={};var s=this;this.setElement('
    '),this.list={};var o=[];"data_collection"==n.type?this.mode="collection":n.multiple?this.mode="multiple":this.mode="single",this.current=this.mode,this.list={};var l=t.textify(n.extensions),c="No dataset available.";l&&(c="No "+l+" dataset available.");var d="No dataset list available.";if(l&&(d="No "+l+" dataset collection available."),"single"==this.mode&&(o.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"}),this.select_single=new e.Select.View({optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.single={field:this.select_single,type:"hda"}),("single"==this.mode||"multiple"==this.mode)&&(o.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"}),this.select_multiple=new e.Select.View({multiple:!0,searchable:!1,optional:n.optional,error_text:c,onchange:function(){s.trigger("change")}}),this.list.multiple={field:this.select_multiple,type:"hda"}),"single"==this.mode||"multiple"==this.mode||"collection"==this.mode){o.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});var h="multiple"==this.mode;this.select_collection=new e.Select.View({error_text:d,multiple:h,searchable:!1,optional:n.optional,onchange:function(){s.trigger("change")}}),this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:o,onchange:function(t){s.current=t,s.refresh(),s.trigger("change")}}),this.$batch=a(this.template_batch());var u=r.size(this.list),p=0;u>1&&(this.$el.append(this.button_type.$el),p=Math.max(0,35*r.size(this.list))+"px");for(var f in this.list)this.$el.append(this.list[f].field.$el.css({"margin-left":p}));this.$el.append(this.$batch.css({"margin-left":p})),this.update(n.data),void 0!==this.options.value&&this.value(this.options.value),this.refresh(),this.on("change",function(){n.onchange&&n.onchange(s.value())})},wait:function(){for(var t in this.list)this.list[t].field.wait()},unwait:function(){for(var t in this.list)this.list[t].field.unwait()},update:function(t){function e(t,e){if(t){var n=[];for(var s in e){var o=e[s];n.push({label:o.hid+": "+o.name,value:o.id}),i.history[o.id+"_"+o.src]=o}t.update(n)}}var i=this;e(this.select_single,t.hda),e(this.select_multiple,t.hda),e(this.select_collection,t.hdca)},value:function(t){if(void 0!==t)if(t&&t.values)try{var e=[];for(var i in t.values)e.push(t.values[i].id);t&&t.values.length>0&&"hdca"==t.values[0].src?(this.current="collection",this.select_collection.value(e)):"multiple"==this.mode?(this.current="multiple",this.select_multiple.value(e)):(this.current="single",this.select_single.value(e[0]))}catch(n){Galaxy.emit.debug("tools-select-content::value()","Skipped.")}else for(var i in this.list)this.list[i].field.value(null);this.refresh();var s=this._select().value();if(null===s)return null;if(s instanceof Array||(s=[s]),0===s.length)return null;var o={batch:this._batch(),values:[]};for(var i in s){var a=this.history[s[i]+"_"+this.list[this.current].type];if(!a)return null;o.values.push(a)}return o.values.sort(function(t,e){return t.hid-e.hid}),o},refresh:function(){this.button_type.value(this.current);for(var t in this.list){var e=this.list[t].field.$el;this.current==t?e.show():e.hide()}this._batch()?this.$batch.show():this.$batch.hide()},_select:function(){return this.list[this.current].field},_batch:function(){if("collection"==this.current){var t=this.history[this._select().value()+"_hdca"];if(t&&t.map_over_type)return!0}return"single"!=this.current&&"single"==this.mode?!0:!1},template_batch:function(){return'
    This is a batch mode input field. A separate job will be triggered for each dataset.
    '}});return{View:n}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3))},function(t,e,i){var n,s;(function(o,a,r){n=[i(4),i(11),i(7),i(42),i(38)],s=function(t,e,i,n,s){return o.View.extend({initialize:function(e){this.options=t.merge(e,{initial_errors:!1,cls:"ui-portlet-limited",icon:""}),this.modal=parent.Galaxy&&parent.Galaxy.modal||new i.Modal.View,this.setElement("
    "),this.render()},update:function(t){var e=this;this.data.matchModel(t,function(t,i){var n=e.input_list[t];if(n&&n.options&&!a.isEqual(n.options,i.options)){n.options=i.options;var s=e.field_list[t];if(s.update){var o=[];if(-1!=["data","data_collection","drill_down"].indexOf(n.type))o=n.options;else for(var r in i.options){var l=i.options[r];l.length>2&&o.push({label:l[0],value:l[1]})}s.update(o),s.trigger("change"),Galaxy.emit.debug("form-view::update()","Updating options for "+t)}}})},wait:function(t){for(var e in this.input_list){var i=this.field_list[e],n=this.input_list[e];n.is_dynamic&&i.wait&&i.unwait&&(t?i.wait():i.unwait())}},highlight:function(t,e,i){var n=this.element_list[t];if(n&&(n.error(e||"Please verify this parameter."),this.trigger("expand",t),!i))if(self==top){var s=this.$el.parents().filter(function(){return"auto"==r(this).css("overflow")}).first();s.animate({scrollTop:s.scrollTop()+n.$el.offset().top-50},500)}else r("html, body").animate({scrollTop:n.$el.offset().top-20},500)},errors:function(t){if(this.trigger("reset"),t&&t.errors){var e=this.data.matchResponse(t.errors);for(var i in this.element_list){this.element_list[i];e[i]&&this.highlight(i,e[i],!0)}}},render:function(){var t=this;this.off("change"),this.off("reset"),this.field_list={},this.input_list={},this.element_list={},this.data=new s.Manager(this),this._renderForm(),this.data.create(),this.options.initial_errors&&this.errors(this.options);var e=this.data.checksum();return this.on("change",function(){var i=t.data.checksum();i!=e&&(e=i,t.options.onchange&&t.options.onchange())}),this.on("reset",function(){for(var t in this.element_list)this.element_list[t].reset()}),this},_renderForm:function(){this.message=new i.Message,this.section=new n.View(this,{inputs:this.options.inputs}),r(".tooltip").remove(),this.portlet=new e.View({icon:this.options.icon,title:this.options.title,cls:this.options.cls,operations:this.options.operations,buttons:this.options.buttons,collapsible:this.options.collapsible,collapsed:this.options.collapsed}),this.portlet.append(this.message.$el.addClass("ui-margin-top")),this.portlet.append(this.section.$el),this.$el.empty(),this.$el.append(this.portlet.$el),this.options.message&&this.message.update({persistent:!0,status:"warning",message:this.options.message}),Galaxy.emit.debug("form-view::initialize()","Completed")}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(35),i(46),i(5)],s=function(t,e,i){function n(t){return function(e,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",e=e||{},e.type="dataset_collection"),t.call(this,e,i)}}var s=e.HistoryContentMixin,a=t.ListDatasetCollection,r=t.PairDatasetCollection,l=t.ListPairedDatasetCollection,c=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){a.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(a.prototype.save),toString:function(){return["HistoryListDatasetCollection(",this.get("name"),")"].join("")}}),d=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){r.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(r.prototype.save),toString:function(){return["HistoryPairDatasetCollection(",this.get("name"),")"].join("")}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),initialize:function(t,e){l.prototype.initialize.call(this,t,e),s.initialize.call(this,t,e)},save:n(l.prototype.save),toString:function(){return["HistoryListPairedDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:c,HistoryPairDatasetCollection:d,HistoryListPairedDatasetCollection:h}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(3))},function(t,e,i){var n,s;(function(o,a){n=[i(15),i(6),i(5)],s=function(t,e,i){var n="history",s=function(t,e){return[t,e].join("-")},r={defaults:{history_id:null,history_content_type:null,hid:null,visible:!0},idAttribute:"type_id",constructor:function(t,e){t.type_id=s(t.history_content_type,t.id),this.debug("HistoryContentMixin.constructor:",t.type_id),o.Model.apply(this,arguments)},_typeIdStr:function(){return s(this.get("history_content_type"),this.get("id"))},initialize:function(t,e){this.on("change:id",this._createTypeId)},_createTypeId:function(){this.set("type_id",this._typeIdStr())},isNew:function(){return!this.get("id")},hidden:function(){return!this.get("visible")},isVisible:function(t,e){var i=!0;return t||!this.get("deleted")&&!this.get("purged")||(i=!1),e||this.get("visible")||(i=!1),i},urlRoot:Galaxy.root+"api/histories/",url:function(){var t=this.urlRoot+this.get("history_id")+"/contents/"+this.get("history_content_type")+"s/"+this.get("id");return t},hide:function(t){return this.get("visible")?this.save({visible:!1},t):a.when()},unhide:function(t){return this.get("visible")?a.when():this.save({visible:!0},t)},toString:function(){var t=this.get("id")||"";return this.get("name")&&(t=this.get("hid")+' :"'+this.get("name")+'",'+t),"HistoryContent("+t+")"}},l=o.Model.extend(e.LoggableMixin).extend(r).extend({_logNamespace:n});return{typeIdStr:s,HistoryContentMixin:r,HistoryContent:l}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(o,a,r){n=[i(46),i(96),i(45),i(6),i(5)], -s=function(t,e,i,n,s){var l="history",c=o.Collection.extend(n.LoggableMixin).extend({_logNamespace:l,model:function(t,n){if("dataset"===t.history_content_type)return new e.HistoryDatasetAssociation(t,n);if("dataset_collection"===t.history_content_type){switch(t.collection_type){case"list":return new i.HistoryListDatasetCollection(t,n);case"paired":return new i.HistoryPairDatasetCollection(t,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(t,n)}return{validationError:"Unknown collection_type: "+t.history_content_type}}return{validationError:"Unknown history_content_type: "+t.history_content_type}},initialize:function(t,e){e=e||{},this.historyId=e.historyId,this.model.prototype.idAttribute="type_id",this.on("all",function(){this.debug(this+".event:",arguments)})},urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},ids:function(){return this.map(function(t){return t.get("id")})},notReady:function(){return this.filter(function(t){return!t.inReadyState()})},running:function(){var t=[];return this.each(function(e){var i=!e.inReadyState();i&&t.push(e.get("id"))}),t},getByHid:function(t){return a.first(this.filter(function(e){return e.get("hid")===t}))},getVisible:function(t,e,i){i=i||[],this.debug("checking isVisible");var n=new c(this.filter(function(i){return i.isVisible(t,e)}));return a.each(i,function(t){a.isFunction(t)&&(n=new c(n.filter(t)))}),n},hidden:function(){function t(t){return t.hidden()}return new c(this.filter(t))},deleted:function(){function t(t){return t.get("deleted")}return new c(this.filter(t))},haveDetails:function(){return this.all(function(t){return t.hasDetails()})},fetchAllDetails:function(t){t=t||{};var e={details:"all"};return t.data=t.data?a.extend(t.data,e):e,this.fetch(t)},ajaxQueue:function(t,e){var i=r.Deferred(),n=this.length,s=[];if(!n)return i.resolve([]),i;var o=this.chain().reverse().map(function(a,r){return function(){var l=t.call(a,e);l.done(function(t){i.notify({curr:r,total:n,response:t,model:a})}),l.always(function(t){s.push(t),o.length?o.shift()():i.resolve(s)})}}).value();return o.shift()(),i},isCopyable:function(t){var e=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return a.isObject(t)&&t.id&&a.contains(e,t.model_class)},copy:function(t){var e,i,n;a.isString(t)?(e=t,n="hda",i="dataset"):(e=t.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[t.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,o=r.post(this.url(),{content:e,source:n,type:i}).done(function(t){s.add([t])}).fail(function(t,a,r){s.trigger("error",s,o,{},"Error copying contents",{type:i,id:e,source:n})});return o},matches:function(t){return this.filter(function(e){return e.matches(t)})},set:function(e,i){e=a.isArray(e)?e:[e],a.each(e,function(e){e.type_id&&e.get&&e.get("type_id")||(e.type_id=t.typeIdStr(e.history_content_type,e.id))}),o.Collection.prototype.set.call(this,e,i)},createHDCA:function(t,e,n,s){var o=this,a={list:i.HistoryListDatasetCollection,paired:i.HistoryPairDatasetCollection},r=new a[e]({history_id:this.historyId,name:n,element_identifiers:t});return r.save().done(function(t){o.add(r)}).fail(function(t,e,i){o.trigger("error",t,e,i)})},clone:function(){var t=o.Collection.prototype.clone.call(this);return t.historyId=this.historyId,t},print:function(){var t=this;t.each(function(e){t.debug(e),e.elements&&t.debug(" elements:",e.elements)})},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(3),i(1))},function(t,e,i){var n,s;(function(o,a,r,l){n=[i(6),i(5)],s=function(t,e){var i="list",n=o.View.extend(t.LoggableMixin).extend({_logNamespace:i,initialize:function(t){this.expanded=t.expanded||!1,this.log(" expanded:",this.expanded),this.fxSpeed=void 0!==t.fxSpeed?t.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(t){var e=this._buildNewRender();return this._setUpBehaviors(e),this._queueNewRender(e,t),this},_buildNewRender:function(){var t=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(t).replaceWith(this._renderDetails().show()),t},_queueNewRender:function(t,e){e=void 0===e?this.fxSpeed:e;var i=this;a(i).queue("fx",[function(t){this.$el.fadeOut(e,t)},function(e){i._swapNewRender(t),e()},function(t){this.$el.fadeIn(e,t)},function(t){this.trigger("rendered",i),t()}])},_swapNewRender:function(t){return this.$el.empty().attr("class",r.isFunction(this.className)?this.className():this.className).append(t.children())},_setUpBehaviors:function(t){t=t||this.$el,t.find("[title]").tooltip({placement:"bottom"})},$details:function(t){return t=t||this.$el,t.find("> .details")},_renderDetails:function(){var t=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(t),t},toggleExpanded:function(t){return t=void 0===t?!this.expanded:t,t?this.expand():this.collapse(),this},expand:function(){var t=this;return t._fetchModelDetails().always(function(){t._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?l.when():this.model.fetch()},_expand:function(){var t=this,e=t._renderDetails();t.$details().replaceWith(e),t.expanded=!0,t.$details().slideDown({duration:t.fxSpeed,step:function(){t.trigger("expanding",t)},complete:function(){t.trigger("expanded",t)}})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var t=this;t.expanded=!1,this.$details().slideUp({duration:t.fxSpeed,step:function(){t.trigger("collapsing",t)},complete:function(){t.trigger("collapsed",t)}})}}),s=n.extend(t.mixin(t.SelectableViewMixin,t.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(e){n.prototype.initialize.call(this,e),t.SelectableViewMixin.initialize.call(this,e),t.DraggableViewMixin.initialize.call(this,e),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(t){t?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var t=n.prototype._buildNewRender.call(this);return t.children(".warnings").replaceWith(this._renderWarnings()),t.children(".title-bar").replaceWith(this._renderTitleBar()),t.children(".primary-actions").append(this._renderPrimaryActions()),t.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),t},_swapNewRender:function(t){return n.prototype._swapNewRender.call(this,t),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var t=this,e=a('
    '),i=t.model.toJSON();return r.each(t.templates.warnings,function(n){e.append(a(n(i,t)))}),e},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(t){t.stopPropagation(),t.altKey?(this.toggleSelect(t),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(t){var e=32,i=13;return!t||"keydown"!==t.type||t.keyCode!==e&&t.keyCode!==i?!0:(this.toggleExpanded(),t.stopPropagation(),!1)},toString:function(){var t=this.model?this.model+"":"(no model)";return"ListItemView("+t+")"}}));s.prototype.templates=function(){var e=t.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=t.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=t.wrapTemplate(['
    ']),o=t.wrapTemplate(['
    ']);return{el:e,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(t){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=t.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=t.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,t),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var t=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,t)},_createFoldoutPanel:function(){var t=this.model,e=this._getFoldoutPanelClass(t),i=this._getFoldoutPanelOptions(t),n=new e(r.extend(i,{model:t}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(t,e){return e=e||this.$("> .details"),this.foldout=t.render(0),t.$("> .controls").hide(),e.append(t.$el)},expand:function(){var t=this;return t._fetchModelDetails().always(function(){"foldout"===t.foldoutStyle?t._expand():"drilldown"===t.foldoutStyle&&t._expandByDrilldown()})},_expandByDrilldown:function(){var t=this;t.foldout.on("close",function(){t.trigger("collapsed:drilldown",t,t.foldout)}),t.trigger("expanded:drilldown",t,t.foldout)}});return c.prototype.templates=function(){var e=t.wrapTemplate(['
    ',"
    "],"collection");return r.extend({},s.prototype.templates,{details:e})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1),i(3),i(1))},function(t,e,i){var n,s;(function(o){n=[i(4),i(60),i(7),i(44),i(23),i(21),i(33)],s=function(t,e,i,n,s,a,r){return n.extend({initialize:function(t){var i=this;n.prototype.initialize.call(this,t),this.deferred=new e,t.inputs?(this._buildForm(t),t.needs_update&&this.deferred.execute(function(t){i._updateModel(t)})):this.deferred.execute(function(e){i._buildModel(e,t,!0)})},remove:function(){var t=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(t),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var i=this;this.options=t.merge(e,this.options),this.options=t.merge({icon:void 0===e.icon&&"fa-wrench"||"",title:""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:this._operations(),onchange:function(){i.deferred.reset(),i.deferred.execute(function(t){i._updateModel(t)})}},this.options),this.options.customize&&this.options.customize(this.options),this.render(),this.options.collapsible||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(e,n,s){var a=this;this.options.id=n.id,this.options.version=n.version;var r="",l={};n.job_id?r=Galaxy.root+"api/jobs/"+n.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+n.id+"/build",Galaxy.params&&Galaxy.params.tool_id==n.id&&(l=o.extend({},Galaxy.params),n.version&&(l.tool_version=n.version))),t.request({type:"GET",url:r,data:l,success:function(t){a._buildForm(t.tool_model||t),!s&&a.message.update({status:"success",message:"Now you are using '"+a.options.name+"' version "+a.options.version+", id '"+a.options.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::initialize()","Initial tool model ready.",t),e.resolve()},error:function(t){var n=t&&t.err_msg||"Uncaught error.";a.$el.is(":empty")?a.$el.prepend(new i.Message({message:n,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal.show({title:"Tool request failed",body:n,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form::initialize()","Initial tool model request failed.",t),e.reject()}})},_updateModel:function(e){var i=this,n=this.options.update_url||Galaxy.root+"api/tools/"+this.options.id+"/build",s={tool_id:this.options.id,tool_version:this.options.version,inputs:o.extend(!0,{},i.data.create())};this.wait(!0),Galaxy.emit.debug("tool-form-base::_updateModel()","Sending current state.",s),t.request({type:"POST",url:n,data:s,success:function(t){i.update(t.tool_model||t),i.options.update&&i.options.update(t),i.wait(!1),Galaxy.emit.debug("tool-form-base::_updateModel()","Received new model.",t),e.resolve()},error:function(t){Galaxy.emit.debug("tool-form-base::_updateModel()","Refresh request failed.",t),e.reject()}})},_operations:function(){var t=this,e=this.options,n=new i.ButtonMenu({icon:"fa-cubes",title:!e.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!e.sustain_version&&e.versions&&e.versions.length>1)for(var o in e.versions){var a=e.versions[o];a!=e.version&&n.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var i=e.id.replace(e.version,this.version),n=this.version;t.deferred.reset(),t.deferred.execute(function(e){t._buildModel(e,{id:i,version:n})})}})}else n.$el.hide();var r=new i.ButtonMenu({icon:"fa-caret-down",title:!e.narrow&&"Options"||null,tooltip:"View available options"});return e.biostar_url&&(r.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/p/new/post/")}}),r.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(e.biostar_url+"/local/search/page/?q="+e.name)}})),r.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+e.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&r.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+e.id+"/download"}}),e.requirements&&e.requirements.length>0&&r.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){this.visible?(this.visible=!1,t.message.update({message:""})):(this.visible=!0,t.message.update({persistent:!0,message:s.requirements(e),status:"info"}))}}),e.sharable_url&&r.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(e.sharable_url)}}),{menu:r,versions:n}},_footer:function(){var t=this.options,e=o("
    ").append(s.help(t));if(t.citations){var i=o("
    "),n=new a.ToolCitationCollection;n.tool_id=t.id;var l=new r.CitationListView({el:i,collection:n});l.render(),n.fetch(),e.append(i)}return e}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(1))},function(t,e,i){var n,s;(function(o,a){n=[i(3),i(20),i(14),i(22),i(64),i(65),i(63),i(66)],s=function(t,e,i,n,s,r,l,c){var d={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},h=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(t){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new h(this.toJSON())},set_value:function(t){this.set("value",t||"")}}),u=o.Collection.extend({model:h}),p=h.extend({}),f=h.extend({set_value:function(t){this.set("value",parseInt(t,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),g=f.extend({set_value:function(t){this.set("value",parseFloat(t))}}),m=h.extend({get_samples:function(){return t.map(this.get("options"),function(t){return t[0]})}});h.subModelTypes={integer:f,"float":g,data:p,select:m};var v=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(e){this.set("inputs",new u(t.map(e.inputs,function(t){var e=h.subModelTypes[t.type]||h;return new e(t)})))},toJSON:function(){var t=o.Model.prototype.toJSON.call(this);return t.inputs=this.get("inputs").map(function(t){return t.toJSON()}),t},remove_inputs:function(t){var e=this,i=e.get("inputs").filter(function(e){return-1!==t.indexOf(e.get("type"))});e.get("inputs").remove(i)},copy:function(t){var e=new v(this.toJSON());if(t){var i=new o.Collection;e.get("inputs").each(function(t){t.get_samples()&&i.push(t)}),e.set("inputs",i)}return e},apply_search_results:function(e){return-1!==t.indexOf(e,this.attributes.id)?this.show():this.hide(),this.is_visible()},set_input_value:function(t,e){this.get("inputs").find(function(e){return e.get("name")===t}).set("value",e)},set_input_values:function(e){var i=this;t.each(t.keys(e),function(t){i.set_input_value(t,e[t])})},run:function(){return this._run()},rerun:function(t,e){return this._run({action:"rerun",target_dataset_id:t.id,regions:e})},get_inputs_dict:function(){var t={};return this.get("inputs").each(function(e){t[e.get("name")]=e.get("value")}),t},_run:function(n){var s=t.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),r=new e.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(t){return"pending"!==t}});return a.when(r.go()).then(function(t){o.resolve(new i.DatasetCollection(t))}),o}});t.extend(v.prototype,d);var _=(o.View.extend({}),o.Collection.extend({model:v})),y=o.Model.extend(d),w=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){t.each(this.attributes.elems,function(t){t.show()}),this.show(),this.set("open",!1)},apply_search_results:function(e){var i,n=!0;t.each(this.attributes.elems,function(t){t instanceof y?(i=t,i.hide()):t instanceof v&&t.apply_search_results(e)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});t.extend(w.prototype,d);var b=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,spinner_url:"",clear_btn_url:"",search_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var t=this.attributes.query;if(t.length");if(t.append(r(this.model.toJSON())),"upload1"===this.model.id)t.find("a").on("click",function(t){t.preventDefault(),Galaxy.upload.show()});else if("Tool"===this.model.get("model_class")){var e=this;t.find("a").on("click",function(t){t.preventDefault();var i=new n.View({id:e.model.id,version:e.model.get("version")});i.deferred.execute(function(){Galaxy.app.display(i)})})}return this.$el.append(t),this}}),$=C.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),S=C.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){C.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(l(this.model.toJSON()));var e=this.$el.find(".toolSectionBody");return t.each(this.model.attributes.elems,function(t){if(t instanceof v){var i=new E({model:t,className:"toolTitle"});i.render(),e.append(i.$el)}else if(t instanceof y){var n=new $({model:t});n.render(),e.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),k=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(c(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(t){return this.model.attributes.clear_key&&this.model.attributes.clear_key===t.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),T=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var t=this,e=new k({model:this.model.get("tool_search")});return e.render(),t.$el.append(e.$el),this.model.get("layout").each(function(e){if(e instanceof w){var i=new S({model:e});i.render(),t.$el.append(i.$el)}else if(e instanceof v){var n=new E({model:e,className:"toolTitleNoSection"});n.render(),t.$el.append(n.$el)}else if(e instanceof y){var s=new $({model:e});s.render(),t.$el.append(s.$el)}}),t.$el.find("a.tool-link").click(function(e){var i=a(this).attr("class").split(/\s+/)[0],n=t.model.get("tools").get(i);t.trigger("tool_link_click",e,n)}),this},handle_search_results:function(){var t=this.model.get("tool_search").get("results");t&&0===t.length?a("#search-no-results").show():a("#search-no-results").hide()}}),D=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(s(this.model.toJSON()))}});o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new T({collection:this.collection}),this.tool_form_view=new D},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var t=this;this.tool_panel_view.on("tool_link_click",function(e,i){e.preventDefault(),t.show_tool(i)})},show_tool:function(t){var e=this;t.fetch().done(function(){e.tool_form_view.model=t,e.tool_form_view.render(),e.tool_form_view.$el.show(),a("#left").width("650px")})}});return{ToolParameter:h,IntegerToolParameter:f,SelectToolParameter:m,Tool:v,ToolCollection:_,ToolSearch:b,ToolPanel:x,ToolPanelView:T,ToolFormView:D}}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,i){var n,s;(function(i,o,a,r){n=[],s=function(){var t=i.View.extend({initialize:function(t,e){this.$button=t,this.$button.size()||(this.$button=o("
    ")),this.options=e||[],this.$button.data("popupmenu",this);var i=this;this.$button.click(function(t){return o(".popmenu-wrapper").remove(),i._renderAndShow(t),!1})},_renderAndShow:function(t){this.render(),this.$el.appendTo("body").css(this._getShownPosition(t)).show(),this._setUpCloseBehavior()},render:function(){if(this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options)),this.options.length){var t=this;this.$el.find("li").each(function(e,i){var n=t.options[e];n.func&&o(this).children("a.popupmenu-option").click(function(e){n.func.call(t,e,n),e.preventDefault()})})}return this},template:function(t,e){return['"].join("")},_templateOptions:function(t){return t.length?a.map(t,function(t){if(t.divider)return'
  • ';if(t.header)return['
  • ',t.html,"
    • "].join("");var e=t.href||"javascript:void(0);",i=t.target?' target="'+t.target+'"':"",n=t.checked?'':"";return['
  • ",n,t.html,"
    • "].join("")}).join(""):"
  • (no options)
    • "},_getShownPosition:function(t){var e=this.$el.width(),i=t.pageX-e/2;return i=Math.min(i,o(document).scrollLeft()+o(window).width()-e-5),i=Math.max(i,o(document).scrollLeft()+5),{top:t.pageY,left:i}},_setUpCloseBehavior:function(){function t(t){if(o(document).off("click.close_popup"),window.parent!==window)try{o(window.parent.document).off("click.close_popup")}catch(i){}else try{o("iframe#galaxy_main").contents().off("click.close_popup")}catch(i){}e.remove()}var e=this;if(o("html").one("click.close_popup",t),window.parent!==window)try{o(window.parent.document).find("html").one("click.close_popup",t)}catch(i){}else try{o("iframe#galaxy_main").contents().one("click.close_popup",t)}catch(i){}},addItem:function(t,e){return e=e>=0?e:this.options.length,this.options.splice(e,0,t),this},removeItem:function(t){return t>=0&&this.options.splice(t,1),this},findIndexByHtml:function(t){for(var e=0;e'},_templateContent:function(){return'
    '},_templateBox:function(t){return'
    '},_template:function(){return'
    Select a color
    '}})}.apply(e,n),!(void 0!==s&&(t.exports=s))}).call(e,i(2),i(1))},function(t,e,n){var s,o;(function(a){s=[n(4),n(25)],o=function(t,e){var n=e.BaseIcons.extend({initialize:function(t){t.type=t.display||"checkbox",t.multiple="checkbox"==t.display,e.BaseIcons.prototype.initialize.call(this,t),this.initial=!0},value:function(t){var i=e.BaseIcons.prototype.value.call(this,t);if(this.initial&&null!==i&&this.header_index){this.initial=!1;var n=i;a.isArray(n)||(n=[n]);for(var s in n){var o=this.header_index[n[s]];for(var r in o)this._setState(o[r],!0)}}return i},_setState:function(t,e){var i=this.$(".button-"+t),n=this.$(".subgroup-"+t);i.data("is_expanded",e),e?(n.fadeIn("fast"),i.removeClass("fa-plus-square"),i.addClass("fa-minus-square")):(n.hide(),i.removeClass("fa-minus-square"),i.addClass("fa-plus-square"))},_templateOptions:function(e){function n(t,e){var i=t.find(".button-"+e);i.on("click",function(){o._setState(e,!i.data("is_expanded"))})}function s(e,r,l){l=l||[];for(i in r){var c=r[i],d=c.options.length>0,h=l.slice(0);o.header_index[c.value]=h.slice(0);var u=a("
    ");if(d){var p=t.uid(),f=a(''),g=a('