Created
September 30, 2013 16:06
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This is the martexplorer main.js hardcoded!
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| (function($) { | |
| /* | |
| * Author: jhsu | |
| * | |
| * This file + required modules contains all the JavaScript to run MartExplorer. | |
| * | |
| * The workflow starts from the biomart.martexplorer.init function, and ends with _stepCallback function. | |
| * | |
| * The _stepCallback function has an array (bound by closure) that maps to each of the four steps. | |
| * Each step callback contains its own specific logic (e.g. Results requires >= 1 attributes, or else | |
| * goes back to Output step) | |
| * | |
| * _elements hold all jQuery DOM elements that are used multiple times | |
| * _state holds current state of the explorer application | |
| * | |
| */ | |
| $.namespace('biomart.martexplorer', function(self) { | |
| var QUERY_CLIENT = 'webbrowser', | |
| QUERY_LIMIT = 1000, | |
| ANIMATION_TIME = 100, | |
| BLOCK_OPTIONS = { | |
| message: '<span class="loading" style="margin: 3px auto"></span>', | |
| css: { padding: '5px', borderColor: '#2e6e9e' }, | |
| overlayCSS: { backgroundColor: '#fff' } | |
| }, | |
| QUERY_RESULTS_OPTIONS = { | |
| paginateBy: 20, | |
| showProgress: true, | |
| animationTime: ANIMATION_TIME, | |
| showLoading: false | |
| }, | |
| SORTABLE_OPTIONS = { | |
| helper: 'clone', | |
| revert: 250, | |
| cursor: 'move', | |
| update: function(ev, ui) { | |
| $.publish('biomart.change'); | |
| if (!ui.item.hasClass('empty')) { | |
| } | |
| } | |
| }, | |
| _urlHash, | |
| _guiContainer, // required (see MartService API document) | |
| _elements = {}, // cache | |
| _dimensions = {}, | |
| // URL query parameters that are not filters (need to know this later) | |
| _nonFilterParams = ['mart', 'step', 'datasets', 'attributes', '_ac', '_fc'], | |
| // callbacks when user navigates to a step | |
| _stepCallback = (function() { | |
| var fn = [ | |
| // Datasets | |
| function(element) { | |
| _elements.filterTree.addClass('hidden'); | |
| _elements.navPrev.addClass('ui-state-disabled'); | |
| _elements.navNext.show(); | |
| _elements.navResults.hide(); | |
| if (biomart._state.queryMart.datasets && biomart._state.queryMart.datasets.length) { | |
| _elements.navNext.removeClass('ui-state-disabled'); | |
| } else { | |
| _elements.navNext.addClass('ui-state-disabled'); | |
| } | |
| if (!_elements.steps.eq(0).data('loaded')) { | |
| } else { | |
| $.publish('biomart.loaded'); | |
| } | |
| }, | |
| // Filters | |
| function(element) { | |
| _elements.filterTree.removeClass('hidden'); | |
| _elements.navPrev.removeClass('ui-state-disabled'); | |
| _elements.navNext.removeClass('ui-state-disabled').show(); | |
| _elements.navResults.hide(); | |
| if (!element.data('loaded')) { | |
| loadFilters(function() { | |
| element.data('loaded', true); | |
| }); | |
| } else { | |
| $.publish('biomart.loaded'); | |
| } | |
| }, | |
| // Output | |
| function(element) { | |
| _elements.attributeTree.removeClass('hidden'); | |
| _elements.navPrev.removeClass('ui-state-disabled'); | |
| _elements.navNext.hide(); | |
| _elements.navResults.show(); | |
| if ($.isEmptyObject(biomart._state.queryMart.attributes)) { | |
| _elements.navResults.addClass('ui-state-disabled'); | |
| } else { | |
| _elements.navResults.removeClass('ui-state-disabled'); | |
| } | |
| if (!element.data('loaded')) { | |
| loadAttributes(function() { | |
| if (!$.isEmptyObject(biomart._state.queryMart.attributes)) { | |
| _elements.navResults.removeClass('ui-state-disabled'); | |
| } | |
| element.data('loaded', true); | |
| }); | |
| } else { | |
| $.publish('biomart.loaded'); | |
| } | |
| }, | |
| function(element) { | |
| _elements.contentWrapper.slideUp(); | |
| _elements.toolbar.slideUp(); | |
| _elements.results.resultsPanel('run', | |
| biomart.utils.hasGroupedMarts() ? biomart._state.mart[0].group : biomart._state.mart.displayName, | |
| $.extend({ | |
| queries: getXml('TSVX', QUERY_LIMIT, true, QUERY_CLIENT), | |
| downloadXml: getXml('TSV', -1, true, QUERY_CLIENT), | |
| martObj: biomart._state.queryMart, | |
| dataAggregation: 'none', | |
| // I'M HARDCODING JUST FOR NOW | |
| displayType: 'network' // instead of 'table' | |
| ///////////////////////// | |
| }, QUERY_RESULTS_OPTIONS)); | |
| $.publish('biomart.loaded'); | |
| } | |
| ]; | |
| return function(index, callback) { | |
| fn[index](_elements.steps.eq(index)); | |
| self.resize(); | |
| if (callback) callback(); | |
| }; | |
| })(); | |
| biomart._state = { | |
| queryMart: {datasets:null, attributes:{}, filters:{}}, | |
| activeStep: 1 | |
| }; | |
| // Invalid filters will show as disabled controls | |
| biomart.renderer.renderInvalid = true; | |
| /* | |
| * Public functions | |
| */ | |
| self.init = function() { | |
| if (!biomart._state.initialized) { | |
| // Initial page load | |
| initElements(); | |
| initNav(); | |
| } else { | |
| // Probably a logout action | |
| _elements.martSelectBox.empty(); | |
| updateParam('mart', null); | |
| updateParam('step', 1); | |
| biomart.resource.cache = {}; | |
| } | |
| biomart.resource.load('gui', function(json) { | |
| var martSelect; | |
| if (!biomart._state.initialized) { | |
| initDimensions(); | |
| } | |
| if (!json.marts) { | |
| biomart.error(); | |
| self.resize(); | |
| return; | |
| } | |
| martSelect = biomart.makeMartSelect(json.marts, { | |
| each: function(mart, selected) { | |
| // If mart not set, default to first | |
| if (selected) { | |
| biomart._state.mart = mart; | |
| $.publish('biomart.change', 'mart', mart); | |
| } else if (!biomart._state.mart) biomart._state.mart = mart; | |
| }, | |
| selected: biomart.params.mart | |
| }); | |
| martSelect | |
| .addClass('mart') | |
| .appendTo(_elements.martSelectBox) | |
| .prettybox(); | |
| initState(); | |
| self.reset(function() { | |
| if (biomart.params.step) self.step(parseInt(biomart.params.step)); | |
| if (!biomart._state.initialized) | |
| attachEvents(); | |
| initData(function() { | |
| _stepCallback(biomart._state.activeStep-1); | |
| biomart._state.initialized = true; | |
| $('#biomart-loading').fadeAndRemove(ANIMATION_TIME); | |
| }); | |
| }); | |
| }, {name: _guiContainer}); | |
| }; | |
| // Reset everything but mart | |
| self.reset = function(callback) { | |
| _elements.steps.each(function() { $(this).data('loaded', false) }); | |
| getDatasets(function() { | |
| if (biomart._state.mart.config) { | |
| biomart._state.queryMart.config = biomart._state.mart.config; | |
| } | |
| updateDatasets(); | |
| if (callback) callback(); | |
| }); | |
| }; | |
| // Update mart from selection and reset | |
| self.restart = function() { | |
| updateMart(biomart._state.mart); | |
| self.refreshParamCache(); | |
| self.reset(); | |
| }; | |
| self.resize = function() { | |
| var h, w; | |
| h = _dimensions.viewportHeight = $(window).height() - 120; | |
| h -= _dimensions.header; | |
| h -= _dimensions.footer; | |
| h -= _dimensions.toolbar; | |
| h -= _dimensions.contentFooter; | |
| _elements.filterContent.height(h-2 + 'px'); | |
| _elements.filterTree.height(h-2 + 'px'); | |
| _elements.attributeContent.height(h-2 + 'px'); | |
| _elements.attributeTree.height(h-2 + 'px'); | |
| _elements.summary.height(h + 'px'); | |
| _elements.main.height(h + 'px'); | |
| _elements.mainSteps.height(h + 'px'); | |
| w = _elements.contentWrapper.outerWidth() - 26; | |
| w -= _dimensions.summaryWidth; | |
| _elements.main.width(w + 'px'); | |
| }; | |
| self.updateNav = function(type) { | |
| var num = biomart._state.activeStep; | |
| _elements.stepInfo.removeClass('ui-active').filter('.step-' + num).addClass('ui-active'); | |
| // step callback is called at end of initialization, so no need to do it here | |
| if (biomart._state.initialized) { | |
| _stepCallback(num-1); | |
| } | |
| }; | |
| self.updateStepInfo = function() { | |
| // Datasets valid | |
| if (biomart._state.queryMart.datasets && biomart._state.queryMart.datasets.length) { | |
| _elements.stepInfo.eq(1).removeClass('ui-state-disabled'); | |
| _elements.stepInfo.eq(2).removeClass('ui-state-disabled'); | |
| } else { | |
| _elements.stepInfo.eq(1).addClass('ui-state-disabled'); | |
| _elements.stepInfo.eq(2).addClass('ui-state-disabled'); | |
| _elements.stepInfo.eq(3).addClass('ui-state-disabled'); | |
| } | |
| // Attributes valid | |
| if (biomart.params.attributes) { | |
| _elements.stepInfo.eq(3).removeClass('ui-state-disabled'); | |
| } else { | |
| _elements.stepInfo.eq(3).addClass('ui-state-disabled'); | |
| } | |
| }; | |
| self.showSubContainer = function() { | |
| if (biomart._state.initialized) { | |
| if (biomart._state.activeStep == 2) { | |
| var node = _elements.filterTree.find('.jstree-leaf'); | |
| if (biomart.params._fc) { | |
| node = node.filter('.' + biomart.params._fc); | |
| } else { | |
| node = node.eq(0); | |
| } | |
| node = node.children('a') | |
| if (!node.hasClass('jstree-clicked')) { | |
| node.click() | |
| } | |
| } else if (biomart._state.activeStep == 3) { | |
| var node = _elements.attributeTree.find('.jstree-leaf'); | |
| if (biomart.params._ac) { | |
| node = node.filter('.' + biomart.params._ac); | |
| } else { | |
| node = node.eq(0); | |
| } | |
| node = node.children('a') | |
| if (!node.hasClass('jstree-clicked')) { | |
| node.click() | |
| } | |
| } | |
| } | |
| }; | |
| self.block = function() { | |
| _elements.content.block(BLOCK_OPTIONS); | |
| }; | |
| self.unblock = function() { | |
| _elements.content.unblock(); | |
| }; | |
| // Goes to a step in the explorer (between 1 and 4) | |
| self.step = function(num) { | |
| if (num < 1 || num > 4) return; | |
| var index = num - 1, | |
| curr; | |
| _elements.steps.eq(biomart._state.activeStep-1).fadeOut({ duration: ANIMATION_TIME }); | |
| curr = _elements.steps.eq(index).fadeIn(); | |
| if (!curr.data('loaded')) self.block(); | |
| biomart._state.activeStep = index + 1; | |
| _elements.filterContent.scrollTop(0); | |
| _elements.attributeContent.scrollTop(0); | |
| $.publish('biomart.change', 'step', num); | |
| }; | |
| self.invalidateResults = function() { | |
| }; | |
| self.refreshParamCache = function() { | |
| // Grab URL info | |
| _urlHash = biomart.url.jsonify(location.href); | |
| _urlHash = biomart.url.jsonify(_urlHash.fragment); // only care about fragment | |
| _guiContainer = _urlHash.path.replace(/\/$/, ''); // clean trailing slash (if exist) | |
| biomart.params = $.deparam(_urlHash.query); | |
| if (biomart._state.initialized && biomart.params.step && biomart.params.step != biomart._state.activeStep) { | |
| self.step(parseInt(biomart.params.step)); | |
| } | |
| }; | |
| self.updateSummary = function(type) { | |
| var item, value, containerName; | |
| switch (type) { | |
| case 'mart': | |
| item = arguments[1]; | |
| _elements.summaryMart.html(['<li>', biomart.utils.hasGroupedMarts() ? item[0].group : item.displayName, '</li>'].join('')); | |
| break; | |
| case 'datasets': | |
| item = arguments[1]; | |
| _elements.summaryDatasets.empty(); | |
| _elements.summaryAttributes | |
| .html(['<li class="empty">', _('empty_value'), '</li>'].join('')); | |
| _elements.summaryFilters | |
| .html(['<li class="empty">', _('empty_value'), '</li>'].join('')); | |
| if (!item.length) { | |
| _elements.summaryDatasets | |
| .empty() | |
| .append(['<li class="empty">', _('empty_value'), '</li>'].join('')); | |
| } else { | |
| for (var i=0, ds; ds=item[i]; i++) { | |
| $(['<li class="', ds.name, '">', | |
| ds.displayName, | |
| '</li>'].join('')) | |
| .appendTo(_elements.summaryDatasets) | |
| .data('item', ds); | |
| } | |
| } | |
| break; | |
| case 'filters': | |
| item = arguments[1]; | |
| value = arguments[2]; | |
| containerName = item['parent'] | |
| _elements.summaryFilters.children('li.empty').remove(); | |
| if ($.isEmptyObject(biomart._state.queryMart.filters)) { | |
| _elements.summaryFilters | |
| .empty() | |
| .append(['<li class="empty">', _('empty_value'), '</li>'].join('')); | |
| } else { | |
| if (value) { | |
| var li = _elements.summaryFilters.children('li.' + biomart.renderer.makeClassName(item.name)), | |
| displayName, value; | |
| if (!li.length) { | |
| li = $(['<li data-container="', containerName, '" class="', biomart.renderer.makeClassName(item.name), '"></li>'].join('')).appendTo(_elements.summaryFilters); | |
| } | |
| li | |
| .data('item', item) | |
| .data('value', value); | |
| if ($.isArray(value)) { | |
| displayName = value[2]; | |
| value = value[1]; | |
| } else { | |
| displayName = item.displayName; | |
| } | |
| li | |
| .html([ | |
| '<span class="key">', displayName, '</span>: ', | |
| '<span class="value">', value, '</span>', | |
| '<span class="ui-icon ui-icon-circle-close" title="Remove"/>', | |
| '<span class="ui-icon ui-icon-circle-arrow-w" title="View in container"/>' | |
| ].join('')); | |
| } else { | |
| _elements.summaryFilters.children('li.' + biomart.renderer.makeClassName(item.name)).addClass('removing').fadeAndRemove(ANIMATION_TIME); | |
| } | |
| } | |
| break; | |
| case 'attributes': | |
| item = arguments[1]; | |
| containerName = item['parent']; | |
| _elements.summaryAttributes.children('li.empty').remove(); | |
| if ($.isEmptyObject(biomart._state.queryMart.attributes)) { | |
| _elements.summaryAttributes.empty(); | |
| $(['<li class="empty">', _('empty_value'), '</li>'].join('')) | |
| .data('item', item) | |
| .appendTo(_elements.summaryAttributes); | |
| } else { | |
| if (arguments[2] /* add */) { | |
| if (!_elements.summaryAttributes.children('li.' + biomart.renderer.makeClassName(item.name)).length) { | |
| $(['<li data-container="', containerName, '" class="', biomart.renderer.makeClassName(item.name), '">', | |
| item.displayName, | |
| '<span class="ui-icon ui-icon-circle-close" title="Remove"/>', | |
| '<span class="ui-icon ui-icon-circle-arrow-w" title="View in container"/>', | |
| '</li>'].join('')) | |
| .data('item', item) | |
| .appendTo(_elements.summaryAttributes); | |
| } | |
| } else { | |
| _elements.summaryAttributes.children('li.' + biomart.renderer.makeClassName(item.name)).addClass('removing').fadeAndRemove(ANIMATION_TIME); | |
| } | |
| } | |
| break; | |
| } | |
| }; | |
| /* | |
| * Helper functions for initialization | |
| */ | |
| function initState() { | |
| for (var k in biomart.params) { | |
| if ($.inArray(k, _nonFilterParams) == -1) { | |
| biomart._state.queryMart.filters[k] = {name:k, value:biomart.params[k]}; | |
| } | |
| } | |
| for (var k in biomart.params) { | |
| if ($.inArray(k, _nonFilterParams) == -1) { | |
| biomart._state.queryMart.filters[k] = { | |
| name: k, | |
| value: biomart.params[k] | |
| }; | |
| } | |
| } | |
| if (biomart.params.attributes) { | |
| var attributes = biomart.params.attributes.split(','); | |
| for (var i=0, a; a=attributes[i]; i++) { | |
| biomart._state.queryMart.attributes[a] = {name:a}; | |
| } | |
| } | |
| } | |
| function initElements() { | |
| // Cache elements for use later and set up any UI widgets | |
| _elements.header = $('#biomart-header'); | |
| _elements.wrapper = $('#biomart-wrapper'); | |
| _elements.filterContent = $('#biomart-filter-content'); | |
| _elements.filterTree = $('#biomart-filter-tree'); | |
| _elements.attributeContent = $('#biomart-attribute-content'); | |
| _elements.attributeTree = $('#biomart-attribute-tree'); | |
| _elements.main = $('#biomart-main'); | |
| _elements.mainSteps = _elements.main.children('div.steps'); | |
| _elements.content = $('#biomart-content'); | |
| _elements.contentWrapper = $('#biomart-content-wrapper'); | |
| _elements.toolbar = $('#biomart-toolbar'); | |
| _elements.stepInfo = $('#biomart-step-info').children(); | |
| _elements.stepsContainer = _elements.content.find('.steps'); | |
| _elements.steps = _elements.content.find('.step'); | |
| _elements.results = $('#biomart-results') | |
| .resultsPanel() | |
| .bind('edit', function() { | |
| _elements.results.resultsPanel('edit'); | |
| _elements.toolbar.slideDown(); | |
| _elements.contentWrapper.slideDown({ | |
| duration: 'fast', | |
| complete: function() { | |
| updateParam('step', biomart._state.activeStep-1); | |
| self.step(biomart._state.activeStep-1); | |
| } | |
| }); | |
| }); | |
| _elements.contentFooter = $('#biomart-content-footer'); | |
| _elements.nav = $('#biomart-navigation'); | |
| _elements.navPrev = _elements.nav.find('a.prev'); | |
| _elements.navNext = _elements.nav.find('a.next'); | |
| _elements.navResults = _elements.nav.find('a.results'); | |
| _elements.footer = $('#biomart-footer'); | |
| _elements.views = null; | |
| _elements.exportForm = $('#biomart-export-form'); | |
| _elements.exportLimit = $('#biomart-export-limit'); | |
| _elements.martSelectBox = $('#biomart-select-mart'); | |
| _elements.datasetSelectBox = $('#biomart-select-dataset'); | |
| _elements.summary = $('#biomart-summary'); | |
| _elements.summaryMart = _elements.summary.find('li.mart > ul'); | |
| _elements.summaryDatasets = _elements.summary.find('li.datasets > ul'); | |
| _elements.summaryFilters = _elements.summary.find('li.filters > ul').sortable(SORTABLE_OPTIONS); | |
| _elements.summaryAttributes = _elements.summary.find('li.attributes > ul').sortable(SORTABLE_OPTIONS); | |
| _elements.viewXmlLink = _elements.summary.find('div.actions'); | |
| _elements.viewXml = $('#biomart-view-xml').dialog({ | |
| modal: true, | |
| autoOpen: false, | |
| width: 600, | |
| height: 350, | |
| resizable: false, | |
| buttons: { | |
| 'Close': function() { | |
| $(this).dialog('close'); | |
| }, | |
| 'Toggle quote-escape': function() { | |
| var limit = parseInt(_elements.exportLimit.val()) || -1, | |
| xml = getXml('TSV', limit, true, ''), | |
| $this = $(this); | |
| if (!$this.data('escaped')) { | |
| xml = xml.replace(/"/g, '\\"'); | |
| $this.data('escaped', true); | |
| } else { | |
| $this.data('escaped', false); | |
| } | |
| _elements.viewXml.children('textarea').val(xml); | |
| } | |
| } | |
| }); | |
| _elements.newButton = $('#biomart-new'); | |
| _elements.noWarningCheckbox = $('#biomart-no-warning'); | |
| _elements.warning = $('#biomart-warning').dialog({ | |
| modal: true, | |
| autoOpen: false, | |
| width: 425, | |
| height: 225, | |
| resizable: false, | |
| buttons: { | |
| 'No': function() { | |
| $(this).dialog('close'); | |
| }, | |
| 'Yes, start new': function() { | |
| if (_elements.noWarningCheckbox[0].checked) { | |
| $.cookie('no_warning', 1, {path: '/', expires: 365}); | |
| } | |
| self.restart(); | |
| $(this).dialog('close'); | |
| } | |
| } | |
| }); | |
| } | |
| function initDimensions() { | |
| _dimensions.header = _elements.header.outerHeight(); | |
| _dimensions.toolbar = _elements.toolbar.outerHeight(); | |
| _dimensions.nav = _elements.nav.outerHeight(); | |
| _dimensions.contentFooter = _elements.contentFooter.outerHeight(); | |
| _dimensions.footer = _elements.footer.outerHeight(); | |
| _dimensions.summaryWidth = _elements.summary.outerWidth(); | |
| $(window).bind('resize.martexplorer', self.resize); | |
| } | |
| function initNav() { | |
| _elements.nav.delegate('a', 'click.martexplorer', function() { | |
| var $this = $(this), | |
| index; | |
| if (!$this.hasClass('ui-state-disabled')) { | |
| if ($this.hasClass('next')) index = biomart._state.activeStep; | |
| if ($this.hasClass('prev')) index = biomart._state.activeStep - 2; | |
| updateParam('step', index+1); | |
| } | |
| return false; | |
| }); | |
| _elements.stepInfo.bind('click.martexplorer', function() { | |
| var $this = $(this); | |
| if (!$this.hasClass('ui-state-disabled')) { | |
| updateParam('step', $this.attr('data-step-number')); | |
| } | |
| }); | |
| _elements.newButton.bind('click.martexplorer', function() { | |
| if ($.cookie('no_warning') == '1') { | |
| self.restart(); | |
| } else { | |
| _elements.warning.dialog('open'); | |
| } | |
| return false; | |
| }); | |
| } | |
| function initData(callback) { | |
| var queue = new biomart.Queue(_elements.content, 'init'), | |
| hasSetFilters = !$.isEmptyObject(biomart._state.queryMart.filters), | |
| hasSetAttributes = !$.isEmptyObject(biomart._state.queryMart.attributes); | |
| _elements.content.one('queue.done', callback); | |
| if (hasSetFilters) { | |
| queue.queue(function() { | |
| var params = {datasets: biomart._state.queryMart.datasets.join(',')}; | |
| if (biomart._state.queryMart.config) | |
| params.config = biomart._state.queryMart.config; | |
| biomart.resource.load('filters', function(json) { | |
| for (var i=0, f, v; f=json[i]; i++) { | |
| if (v = biomart._state.queryMart.filters[f.name]) { | |
| $.publish('biomart.change', 'filters', f, v.value); | |
| } | |
| } | |
| queue.dequeue(); | |
| }, params); | |
| }); | |
| } | |
| if (hasSetAttributes) { | |
| queue.queue(function() { | |
| var params = {datasets: biomart._state.queryMart.datasets.join(',')}; | |
| if (biomart._state.queryMart.config) | |
| params.config = biomart._state.queryMart.config; | |
| biomart.resource.load('attributes', function(json) { | |
| for (var i=0, a; a=json[i]; i++) { | |
| if (a.selected || biomart._state.queryMart.attributes[a.name]) { | |
| $.publish('biomart.change', 'attributes', a, true); | |
| } | |
| } | |
| queue.dequeue(); | |
| }, params); | |
| }); | |
| } | |
| queue.dequeue(); | |
| } | |
| function attachEvents() { | |
| // Mart changed | |
| _elements.steps.eq(0).delegate('select.mart', 'change.martexplorer', function(ev) { | |
| updateMart($(this).children().eq(this.selectedIndex).data('mart')); | |
| self.refreshParamCache(); | |
| self.reset(); | |
| }); | |
| // Dataset changed | |
| _elements.steps.eq(0).delegate('select.datasets', 'change.martexplorer', function(ev) { | |
| updateDatasets(); | |
| }); | |
| // Filters changed | |
| _elements.filterContent | |
| .delegate('.filter-container', 'removefilter', function(ev) { | |
| biomart.clearFilter($(this), function(item) { | |
| removeQueryFilter(item); | |
| }); | |
| }) | |
| .delegate('.filter-container', 'addfilter', function(ev) { | |
| var $div = $(this), | |
| $box = $div.children('input.checkbox'), | |
| name = $div.attr('filter-name'), | |
| value = biomart.validator.filter($div), | |
| valid = false, | |
| item = $div.data('item'); | |
| if ($.isArray(value)) valid = !!value[0] && !!value[1]; | |
| else valid = !!value; | |
| if (valid) { | |
| $div.addClass('ui-active'); | |
| setQueryFilter(item, value); | |
| } else { | |
| $div.removeClass('ui-active'); | |
| removeQueryFilter(item); | |
| } | |
| }); | |
| // attributes changed | |
| _elements.attributeContent | |
| .delegate('.attribute-container', 'addattribute', function(ev) { | |
| var item = $(this).addClass('ui-active').data('item'); | |
| addQueryAttribute(item); | |
| }) | |
| .delegate('.attribute-container', 'removeattribute', function(ev) { | |
| var item = $(this).removeClass('ui-active').data('item'); | |
| removeQueryAttribute(item); | |
| }); | |
| // URL fragment changed | |
| $(window).bind('hashchange', self.refreshParamCache); | |
| // View XML function | |
| _elements.viewXmlLink.bind('click.martexplorer', function() { | |
| var limit = parseInt(_elements.exportLimit.val()) || -1, | |
| xml = getXml('TSV', limit, true, ''); | |
| _elements.viewXml.children('textarea').val(xml); | |
| _elements.viewXml.data('escaped', false).dialog('open'); | |
| }); | |
| _elements.summary | |
| .delegate('span.ui-icon-circle-close', 'click.martexplorer', function(ev) { | |
| var $target = $(ev.target), | |
| $li = $target.parent(), | |
| item = $li.data('item'); | |
| if (item.type) { | |
| // Filter | |
| removeQueryFilter(item); | |
| (function(div) { | |
| if (div.data('loaded')) { | |
| div.find('.' + biomart.renderer.makeClassName(item.name)) | |
| .find('span.ui-icon-circle-close').trigger('click'); | |
| } | |
| })(_elements.steps.eq(1)); | |
| } else { | |
| // Attribute | |
| removeQueryAttribute(item); | |
| (function(div) { | |
| if (div.data('loaded')) { | |
| div.find('.' + biomart.renderer.makeClassName(item.name)) | |
| .removeClass('ui-active') | |
| .find('input.checkbox').attr('checked', false); | |
| } | |
| })(_elements.steps.eq(2)); | |
| } | |
| }) | |
| .delegate('span.ui-icon-circle-arrow-w', 'click.martexplorer', function(ev) { | |
| var $target = $(ev.target), | |
| $li = $target.parent(), | |
| item = $li.data('item'), | |
| ancestor = $li.parent().closest('li'); | |
| if (ancestor.hasClass('filters')) { | |
| showFilterContainer($li.attr('data-container'), biomart.renderer.makeClassName(item.name)); | |
| } else { | |
| showAttributeContainer($li.attr('data-container'), biomart.renderer.makeClassName(item.name)); | |
| } | |
| }); | |
| } | |
| /* | |
| * Functions for updating user selections | |
| */ | |
| function updateParam(name, value) { | |
| var newUrlHash = biomart.url.jsonify(location.href); | |
| if (value) biomart.params[name] = value; | |
| else delete biomart.params[name]; | |
| _urlHash.query = $.param(biomart.params); | |
| newUrlHash.fragment = biomart.url.stringify(_urlHash); | |
| location = biomart.url.stringify(newUrlHash); | |
| } | |
| function updateMart(item) { | |
| var name; | |
| biomart._state.mart = item; | |
| if ($.isArray(item)) { | |
| name = item[0].group; | |
| } else { | |
| name = item.name; | |
| } | |
| // reset all selections | |
| biomart._state.queryMart = { dataset: null, attributes:{}, filters: {} }; | |
| updateParam('mart', name); | |
| updateParam('datasets', null); | |
| updateParam('attributes', null); | |
| updateParam('filters', null); | |
| updateParam('step', 1); | |
| $.publish('biomart.change', 'mart', item); | |
| } | |
| function updateDatasets() { | |
| var selected = [], | |
| items = [], | |
| active = _elements.datasetSelect.children('option:selected'); | |
| for (var i=0, n=active.length, curr; i<n; i++) { | |
| curr = active.eq(i); | |
| selected.push(curr.attr('value')); | |
| items.push(curr.data('item')); | |
| } | |
| biomart._state.queryMart.datasets = selected; | |
| if (biomart.utils.hasGroupedMarts) { | |
| var ds = items[0]; | |
| if (ds && ds.mart.config) { | |
| biomart._state.queryMart.config = ds.mart.config; | |
| } else { | |
| delete biomart._state.queryMart.config; | |
| } | |
| } | |
| // When app has initialized, we need to clear all attributes and filters from URL | |
| // Otherwise they are present from previous "saved" state | |
| if (biomart._state.initialized) { | |
| biomart._state.queryMart.filters = {}; | |
| biomart._state.queryMart.attributes = {}; | |
| biomart._state.activeStep = 1; | |
| _elements.steps.eq(1).data('loaded', false); | |
| _elements.steps.eq(2).data('loaded', false); | |
| _elements.filterTree.jstree('destroy') | |
| _elements.filterContent.empty(); | |
| _elements.attributeTree.jstree('destroy'); | |
| _elements.attributeContent.empty(); | |
| updateParam('datasets', selected.join(',')); | |
| updateParam('attributes', null); | |
| for (var k in biomart.params) { | |
| if ($.inArray(k, _nonFilterParams) == -1) { | |
| updateParam(k, null); | |
| } | |
| } | |
| } | |
| $.publish('biomart.change', 'datasets', items); | |
| } | |
| function setQueryFilter(item, value) { | |
| biomart._state.queryMart.filters[item.name] = {name: item.name, value: value}; | |
| updateParam(item.name, value); | |
| $.publish('biomart.change', 'filters', item, value); | |
| } | |
| function removeQueryFilter(item) { | |
| delete biomart._state.queryMart.filters[item.name]; | |
| updateParam(item.name, null); | |
| $.publish('biomart.change', 'filters', item, null); | |
| } | |
| function addQueryAttribute(item) { | |
| biomart._state.queryMart.attributes[item.name] = {name: item.name}; | |
| updateAttributeParam(); | |
| $.publish('biomart.change', 'attributes', item, true); | |
| } | |
| function removeQueryAttribute(item) { | |
| delete biomart._state.queryMart.attributes[item.name]; | |
| updateAttributeParam(); | |
| $.publish('biomart.change', 'attributes', item, false); | |
| } | |
| function updateAttributeParam() { | |
| var newAttributes = []; | |
| for (var name in biomart._state.queryMart.attributes) { | |
| newAttributes.push(name); | |
| } | |
| updateParam('attributes', newAttributes.join(',')); | |
| } | |
| /* | |
| * Functions for fetching configurations and data | |
| */ | |
| function getDatasets(callback) { | |
| var martParam, | |
| resource; | |
| if (!biomart.utils.hasGroupedMarts()) { | |
| martParam = biomart._state.mart.name; | |
| resource = 'datasets'; | |
| } else { | |
| martParam = $.map(biomart._state.mart, function(m) { return m.name }); | |
| martParam = martParam.join(','); | |
| resource = 'datasets/mapped'; | |
| } | |
| biomart.resource.load(resource, function(json) { | |
| var selected = false, | |
| dsArr = biomart.params.datasets ? biomart.params.datasets.split(',') : [], | |
| multiple = false, | |
| isMapped = biomart.utils.hasGroupedMarts(); | |
| if (!isMapped) { | |
| multiple = biomart._state.mart.operation == biomart.OPERATION.MULTI_SELECT; | |
| } | |
| if (_elements.datasetSelect) { | |
| _elements.datasetSelect.prettybox('destroy').remove(); | |
| } | |
| _elements.datasetSelect = $(['<select ', multiple ? 'multiple size="10"' : '', ' class="datasets" id="', | |
| biomart.uuid() , '"/>'].join('')).appendTo(_elements.datasetSelectBox); | |
| if (!isMapped) { | |
| for (var i=0, d; d=json[i]; i++) { | |
| if (!d.isHidden) { | |
| d.mart = biomart._state.mart; | |
| selected = (dsArr.length && $.inArray(d.name, dsArr) != -1) || (!dsArr.length && i==0); | |
| $([ | |
| '<option value="', d.name, '"', selected ? ' selected="selected"' : '', '>', | |
| d.displayName, | |
| '</option>' | |
| ].join('')).data('item', d).appendTo(_elements.datasetSelect); | |
| } | |
| } | |
| } else { | |
| var num = 0; | |
| for (var k in json) { | |
| var datasets = json[k], | |
| mart; | |
| for (var i=0, curr; curr=biomart._state.mart[i]; i++) { | |
| if (curr.name == k) { | |
| mart = curr; | |
| break; | |
| } | |
| } | |
| for (var i=0, ds; ds=datasets[i]; i++) { | |
| selected = (dsArr.length && $.inArray(ds.name, dsArr) != -1) || (num==0); | |
| ds.mart = mart; | |
| $(['<option value="', ds.name, '"', selected ? ' selected="selected"' : '', '>', ds.displayName, '</option>'].join('')) | |
| .data('item', ds) | |
| .appendTo(_elements.datasetSelect); | |
| num++; | |
| } | |
| } | |
| } | |
| if (!multiple) _elements.datasetSelect.prettybox(); | |
| _elements.steps.eq(0).data('loaded', true); | |
| if (callback) callback(); | |
| }, {mart: martParam}); | |
| } | |
| function findContainer(node, name) { | |
| if (node.name == name) return node; | |
| if (node.containers) { | |
| for (var i=0, curr; curr=node.containers[i]; i++) { | |
| var result = findContainer(curr, name); | |
| if (result) return result; | |
| } | |
| } | |
| return null; | |
| } | |
| function loadFilters(callback) { | |
| var params = { | |
| datasets: biomart._state.queryMart.datasets.join(','), | |
| withfilters: true, | |
| withattributes: false | |
| }; | |
| if (biomart._state.queryMart.config) | |
| params.config = biomart._state.queryMart.config; | |
| $.unsubscribeAll('filterchange'); | |
| _elements.steps.eq(1).data('loaded', true); | |
| biomart.resource.load('containers', function(json) { | |
| var root = biomart.utils.processContainer(json); | |
| if (root) { | |
| biomart._state.filtersRoot = json; | |
| root.title = biomart._state.mart.displayName, | |
| root.attr = { | |
| 'class': 'mart ' + biomart._state.mart.name, | |
| mart: biomart._state.mart.name | |
| }; | |
| root.state = 'open'; | |
| if (!_elements.filterTree.hasClass('jstree')) { | |
| _elements.filterTree | |
| .bind('select_node.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj), | |
| $martNode = $node.closest('li.mart'), | |
| martName = $martNode.attr('mart'), | |
| name = $node.attr('container'), | |
| container; | |
| updateParam('_fc', name); | |
| container = findContainer(biomart._state.filtersRoot, name); | |
| if ($node.hasClass('jstree-leaf') && !$node.hasClass('mart')) { | |
| drawFilterContainer(_elements.filterContent.empty(), container); | |
| } | |
| }) | |
| .bind('beforechange.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj); | |
| if ($node.hasClass('jstree-leaf') && !$node.hasClass('mart')) { | |
| return true; | |
| } else if (!$node.hasClass('loader')) { | |
| $.jstree._focused().open_branch($node); | |
| } | |
| return false; | |
| }) | |
| .bind('beforeclose.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj); | |
| if ($node.find('a.clicked').length) { | |
| return false; | |
| } | |
| return true; | |
| }) | |
| .jstree({ | |
| plugins: ['themes', 'json_data', 'ui'], | |
| json_data: { | |
| data: root.children | |
| }, | |
| themes: { | |
| theme: 'default' | |
| } | |
| }); | |
| } | |
| // Small hack to use setTimeout because otherwise the proper styles don't get added for some reason | |
| // Bug in jstree maybe? | |
| setTimeout(function() { | |
| var node = _elements.filterTree.find('.jstree-leaf'); | |
| if (biomart.params._fc) { | |
| node = node.filter('.' + biomart.params._fc); | |
| } else { | |
| node = node.eq(0); | |
| } | |
| node.children('a').click(); | |
| }, 100); | |
| } | |
| if (callback) callback(); | |
| $.publish('biomart.loaded'); | |
| }, params); | |
| } | |
| function drawFilterContainer(element, container, level) { | |
| biomart.renderer.container({ | |
| tagName:'div', | |
| item: container, | |
| mode: biomart.renderer.FILTERS, | |
| selectedFilters: biomart._state.queryMart.filters, | |
| appendTo: element | |
| }); | |
| } | |
| function loadAttributes(callback) { | |
| var params = { | |
| datasets: biomart._state.queryMart.datasets.join(','), | |
| withfilters: false, | |
| withattributes: true | |
| }; | |
| if (biomart._state.queryMart.config) | |
| params.config = biomart._state.queryMart.config; | |
| _elements.steps.eq(2).data('loaded', true); | |
| biomart.resource.load('containers', function(json) { | |
| var root = biomart.utils.processContainer(json); | |
| if (root) { | |
| biomart._state.attributesRoot = json; | |
| root.title = biomart._state.mart.displayName, | |
| root.attr = { | |
| 'class': 'mart ' + biomart._state.mart.name, | |
| mart: biomart._state.mart.name | |
| }; | |
| root.state = 'open'; | |
| if (!_elements.attributeTree.hasClass('jstree')) { | |
| _elements.attributeTree | |
| .bind('select_node.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj), | |
| $martNode = $node.closest('li.mart'), | |
| martName = $martNode.attr('mart'), | |
| name = $node.attr('container'), | |
| container; | |
| updateParam('_ac', name); | |
| container = findContainer(biomart._state.attributesRoot, name); | |
| if ($node.hasClass('jstree-leaf') && !$node.hasClass('mart')) { | |
| drawAttributeContainer(_elements.attributeContent.empty(), container); | |
| } | |
| }) | |
| .bind('beforechange.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj); | |
| if ($node.hasClass('jstree-leaf') && !$node.hasClass('mart')) { | |
| return true; | |
| } else if (!$node.hasClass('loader')) { | |
| $.jstree._focused().open_branch($node); | |
| } | |
| return false; | |
| }) | |
| .bind('beforeclose.jstree', function(ev, data) { | |
| var $node = $(data.rslt.obj); | |
| if ($node.find('a.clicked').length) { | |
| return false; | |
| } | |
| return true; | |
| }) | |
| .jstree({ | |
| plugins: ['themes', 'json_data', 'ui'], | |
| json_data: { | |
| data: root.children | |
| }, | |
| themes: { | |
| theme: 'default' | |
| } | |
| }); | |
| } | |
| // Small hack to use setTimeout because otherwise the proper styles don't get added for some reason | |
| // Bug in jstree maybe? | |
| setTimeout(function() { | |
| var node = _elements.attributeTree.find('.jstree-leaf'); | |
| if (biomart.params._ac) { | |
| node = node.filter('.' + biomart.params._ac); | |
| } else { | |
| node = node.eq(0); | |
| } | |
| node.children('a').click(); | |
| }, 100); | |
| } | |
| $.publish('biomart.loaded'); | |
| }, params); | |
| } | |
| function drawAttributeContainer(element, container, level, extraClassNames) { | |
| biomart.renderer.container({ | |
| tagName:'div', | |
| item: container, | |
| mode: biomart.renderer.ATTRIBUTES, | |
| extraClassNames: extraClassNames || '', | |
| selectedAttributes: biomart.params.attributes ? biomart.params.attributes.split(',') : [], | |
| onAttributeSelect: function(item) { | |
| biomart._state.queryMart.attributes[item.name] = {name:item.name}; | |
| $.publish('biomart.change', 'attributes', item, true); | |
| }, | |
| extras: function(item, element) { | |
| if (item.maxContainers) { | |
| element | |
| .bind('containershow', function(ev, panel) { | |
| var list = panel.find('.attribute-container.ui-active'), | |
| n = list.length; | |
| while (n--) { | |
| addQueryAttribute(list.eq(n).data('item')); | |
| } | |
| }) | |
| .bind('containerhide', function(ev, panel) { | |
| var list = panel.find('.attribute-container.ui-active'), | |
| n = list.length; | |
| while (n--) { | |
| removeQueryAttribute(list.eq(n).data('item')); | |
| } | |
| }); | |
| } | |
| }, | |
| appendTo: element | |
| }); | |
| } | |
| function getXml(renderer, limit, client) { | |
| var mart = {datasets: [], attributes: {}, filters: {}}; | |
| mart.config = biomart._state.queryMart.config; | |
| // Grab selections from summary panel and generate XML | |
| _elements.summaryDatasets.children().each(function() { | |
| var item = $(this).data('item'); | |
| if (item) | |
| mart.datasets.push($(this).data('item').name); | |
| }); | |
| _elements.summaryFilters.children(':not(.removing)').each(function() { | |
| var $this = $(this), | |
| item = $this.data('item'), | |
| value = $this.data('value'), | |
| name; | |
| if (item) { | |
| if ($.isArray(value)) { | |
| name = value[0]; | |
| value = value[1]; | |
| } else { | |
| name = item.name; | |
| } | |
| mart.filters[name] = {name: name, value: value}; | |
| } | |
| }); | |
| _elements.summaryAttributes.children(':not(.removing)').each(function() { | |
| var item = $(this).data('item'); | |
| if (item) { | |
| mart.attributes[item.name] = {name: item.name}; | |
| } | |
| }); | |
| return biomart.query.compile('XML', mart, renderer, limit, true, client); | |
| } | |
| function showFilterContainer(containerName, filterName) { | |
| updateParam('_fc', containerName); | |
| updateParam('step', 2); | |
| _stepCallback(1); | |
| } | |
| function showAttributeContainer(containerName, attributeName) { | |
| updateParam('_ac', containerName); | |
| updateParam('step', 3); | |
| _stepCallback(2); | |
| } | |
| }); | |
| /* | |
| * Bind callbacks to events | |
| * | |
| * The ordering here is very important! | |
| */ | |
| $.subscribe('biomart.init', biomart.martexplorer, 'refreshParamCache'); | |
| $.subscribe('biomart.init', biomart.martexplorer, 'init'); | |
| $.subscribe('biomart.loaded', biomart.martexplorer, 'unblock'); | |
| $.subscribe('biomart.loaded', biomart.martexplorer, 'updateStepInfo'); | |
| $.subscribe('biomart.loaded', biomart.martexplorer, 'showSubContainer'); | |
| $.subscribe('biomart.change', biomart.martexplorer, 'updateSummary'); | |
| $.subscribe('biomart.change', biomart.martexplorer, 'invalidateResults'); | |
| $.subscribe('biomart.change', biomart.martexplorer, 'updateNav'); | |
| $.subscribe('biomart.restart', biomart.martexplorer, 'init'); | |
| })(jQuery); | |
| biomart.error = function() { | |
| $('#biomart-main').html('<p class="error">An error has occurred. You can try refreshing this page or go back to the <a href="../">landing page</a>.'); | |
| $('#biomart-content').unblock(); | |
| $('#biomart-loading').fadeAndRemove(); | |
| }; |
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