app/index.html
<!doctype html>
<html class="no-js" lang="">
<head>
<meta charset="utf-8">
<!-- This file shouldn't be included in cBioPortal -->
<!-- build:js(.) scripts/iviz-vendor-cbio.js -->
<script src="/bower_components/jquery/jquery.min.js"></script>
<script src="/bower_components/jquery-ui/ui/jquery-ui.js"></script>
<script src="/bower_components/bootstrap-sass/assets/javascripts/bootstrap.js"></script>
<!-- endbuild -->
<!-- build:js(.) scripts/iviz-vendor.js -->
<script src="/bower_components/vue/dist/vue.js"></script>
<script src="/bower_components/modernizr/modernizr.js"></script>
<script src="/bower_components/chosen/chosen.jquery.min.js"></script>
<script src="/bower_components/datatables/media/js/jquery.dataTables.js"></script>
<script src="/bower_components/d3/d3.min.js"></script>
<script src="/bower_components/crossfilter2/crossfilter.min.js"></script>
<script src="/bower_components/dcjs/dc.js"></script>
<script src="/bower_components/classie/classie.js"></script>
<script src="/bower_components/get-style-property/get-style-property.js"></script>
<script src="/bower_components/get-size/get-size.js"></script>
<script src="/bower_components/eventie/eventie.js"></script>
<script src="/bower_components/eventEmitter/EventEmitter.js"></script>
<script src="/bower_components/unipointer/unipointer.js"></script>
<script src="/bower_components/unidragger/unidragger.js"></script>
<script src="/bower_components/draggabilly/draggabilly.js"></script>
<script src="/bower_components/doc-ready/doc-ready.js"></script>
<script src="/bower_components/matches-selector/matches-selector.js"></script>
<script src="/bower_components/fizzy-ui-utils/utils.js"></script>
<script src="/bower_components/outlayer/item.js"></script>
<script src="/bower_components/outlayer/outlayer.js"></script>
<script src="/bower_components/packery/dist/packery.pkgd.js"></script>
<script src="/bower_components/underscore/underscore.js"></script>
<script src="/bower_components/ev-emitter/ev-emitter.js"></script>
<script src="/bower_components/imagesloaded/imagesloaded.js"></script>
<script src="/bower_components/qtip2/jquery.qtip.js"></script>
<script src="/bower_components/qtip2/basic/jquery.qtip.js"></script>
<script src="/bower_components/clipboard/dist/clipboard.js"></script>
<script src="/bower_components/plotly.js/dist/plotly.min.js"></script>
<script src="/bower_components/react/react.js"></script>
<script src="/bower_components/react/react-dom.js"></script>
<script src="/bower_components/fixed-data-table/dist/fixed-data-table.min.js"></script>
<script src="/bower_components/jstat/dist/jstat.min.js"></script>
<script src="/bower_components/backbone/backbone.js"></script>
<script src="/bower_components/remarkable-bootstrap-notify/bootstrap-notify.js"></script>
<script src="/bower_components/progressbar.js/dist/progressbar.min.js"></script>
<!-- endbuild -->
<!-- build:css(.) styles/iviz-vendor.css -->
<link rel="stylesheet" href="/.tmp/styles/vendor.css"/>
<!-- bower:css -->
<link rel="stylesheet" href="/bower_components/datatables/media/css/jquery.dataTables.css" />
<link rel="stylesheet" href="/bower_components/dcjs/dc.css" />
<link rel="stylesheet" href="/bower_components/qtip2/jquery.qtip.css" />
<link rel="stylesheet" href="/bower_components/fixed-data-table/dist/fixed-data-table.min.css" />
<!-- endbower -->
<!-- endbuild -->
<!-- build:css(.tmp) styles/iviz.css -->
<link rel="stylesheet" href="styles/main.css"/>
<!-- endbuild -->
<!-- build:js scripts/cbio-vendor.js -->
<script src="_components/FileSaver.min.js"></script>
<script src="_components/cbio-util.js"></script>
<script src="_components/download-util.js"></script>
<script src="_components/MutatedGeneCNATable.js"></script>
<script src="scripts/model/dataProxy.js"></script>
<script src="_components/cbioportal-client.js"></script>
<!-- endbuild -->
<!-- build:js scripts/iviz.js -->
<script src="scripts/session/sessionEvent.js"></script>
<script src="scripts/session/sessionServices.js"></script>
<script src="scripts/session/sessionUtil.js"></script>
<script src="_components/Notification.js"></script>
<script src="_components/GeneValidator.js"></script>
<script src="_components/QueryByGeneUtil.js"></script>
<script src="_components/QueryByGeneTextArea.js"></script>
<script src="scripts/main.js"></script>
<script src="scripts/vueCore.js"></script>
<script src="scripts/controller/util.js"></script>
<script src="scripts/controller/priorityManager.js"></script>
<script src="scripts/views/mainTemplate.js"></script>
<script src="scripts/views/chartGroupTemplate.js"></script>
<script src="scripts/views/individualChartTemplate.js"></script>
<script src="scripts/views/components/generalChart.js"></script>
<script src="scripts/views/components/chartOperationsHeader.js"></script>
<script src="scripts/views/components/header/manageCharts.js"></script>
<script src="scripts/views/components/header/breadCrumbTemplate.js"></script>
<script src="scripts/views/components/pieChart/pieChart.js"></script>
<script src="scripts/views/components/pieChart/pieChartTemplate.js"></script>
<script src="scripts/views/components/barChart/barChart.js"></script>
<script src="scripts/views/components/barChart/barChartTemplate.js"></script>
<script src="scripts/views/components/scatterPlot/scatterPlot.js"></script>
<script src="scripts/views/components/scatterPlot/scatterPlotTemplate.js"></script>
<script src="scripts/views/components/survivalChart/main.js"></script>
<script src="scripts/views/components/survivalChart/template.js"></script>
<script src="scripts/views/components/survivalChart/components/kmEstimator.js"></script>
<script src="scripts/views/components/survivalChart/components/logRankTest.js"></script>
<script src="scripts/views/components/survivalChart/components/curve.js"></script>
<script src="scripts/views/components/survivalChart/proxy.js"></script>
<script src="scripts/views/components/dataTable/tableView.js"></script>
<script src="scripts/views/components/dataTable/tableViewTemplate.js"></script>
<script src="scripts/views/components/customPlots/CaseDialogBox.js"></script>
<script src="scripts/views/components/error.js"></script>
<script src="scripts/views/components/shareVirtualStudy/shareVirtualStudy.js"></script>
<script src="scripts/views/components/virtualStudy/virtualStudy.js"></script>
<script src="scripts/views/components/progressBar/progressBar.js"></script>
<!-- endbuild -->
</head>
<body>
<div class="container-fluid" id="complete-screen">
<nav class="navbar navbar-default navbar-fixed-top" v-if="!failedToInit.status">
<div id="main-header" style="display: none" :class="{show:!isloading}">
<div id="iviz-header-left">
<div class="iviz-header-left-case iviz-header-item">
<span class="name">Selected:</span>
<span class="content">
<span>{{ selectedSamplesNum }} samples / {{ selectedPatientsNum }} patients</span>
</span>
</div>
<virtual-study class="iviz-header-item" v-if="showShareButton || showSaveButton" :show-share-button="showShareButton"
:show-save-button="showSaveButton" :stats="stats"
:update-stats.sync="updateStats"></virtual-study>
<span id="iviz-header-left-patient-select" class="iviz-header-button iviz-header-item"
@click="openCases" class="number"
role="button" tabindex="0" style="display: block;"><i class="fa fa-user-circle-o" aria-hidden="true"></i></span>
<span id="iviz-header-left-case-download" class="iviz-header-button iviz-header-item" @click="downloadCaseData()"
role="button"
tabindex="0" :disabled="downloadingSelected">
<i v-if="!downloadingSelected" class="fa fa-download" alt="download"></i>
<i v-if="downloadingSelected" class="fa fa-spinner fa-spin"></i></span>
<span id="query-by-gene-span" class="iviz-header-item">
<textarea id="query-by-gene-textarea" class="expand expandFocusOut" rows="1" cols="10"></textarea>
</span>
<span class="iviz-header-arrow iviz-header-item">
<i class="fa fa-arrow-right fa-lg" aria-hidden="true"></i>
</span>
<input type="button" id="iviz-header-left-1" value="Query" class="iviz-header-button iviz-header-item" style="display: block;"
v-on:click="submitForm">
<custom-case-input class="iviz-header-item" :stats="stats" :update-stats.sync="updateStats"></custom-case-input>
<select id="iviz-add-chart" class="chosen-select iviz-header-item"
v-select :charts="charts" v-if="showDropDown">
<option id='' value="">Add Chart</option>
<option id="{{data.attr_id}}" v-if="!data.show" value="{{data.attr_id}}" v-for="(index,data) in charts">
{{data.display_name}}
</option>
</select>
</div>
<div id="breadcrumbs_container" v-if="hasfilters">
<div style="float:left;">
<span class="breadcrumb_container">Your selections: </span>
</div>
<span class="breadcrumb_container"
v-if="customfilter.patientUids.length>0||customfilter.sampleUids.length>0">
<span>{{customfilter.display_name}}</span>
<i class="fa fa-times breadcrumb_remove"
@click="clearAllCharts(true)"></i>
</span>
<div style="float:left" v-for="group in groups">
<bread-crumb :attributes.sync="item"
:filters.sync="item.filter" v-for="(index1, item) in group.attributes"
v-if="item.filter.length>0"></bread-crumb>
</div>
<div style="float:left">
<button type='button' @click="clearAllCharts(true)"
class="btn btn-default btn-xs">Clear All
</button>
</div>
</div>
</div>
</nav>
<div :class="{'start-loading': showScreenLoad}" v-if="!failedToInit.status">
<div class="grid" id="main-grid" v-show="!isloading">
<main-template :groups.sync="groups" :redrawgroups.sync="redrawgroups"
:selectedpatient-uIDs.sync="selectedpatientUIDs"
:selectedsample-uIDs.sync="selectedsampleUIDs"
:hasfilters.sync="hasfilters"
:customfilter.sync="customfilter"
:showed-survival-plot="showedSurvivalPlot"
:clear-all="clearAll"></main-template>
</div>
<progress-bar div-id="study-view-summary-page-pb" :status="studyViewSummaryPagePBStatus" v-show="isloading"></progress-bar>
</div>
<error container-id="fail-to-init" v-if="failedToInit.status" :message="failedToInit.message"></error>
</div>
</body>
<script>
$(document).ready(function() {
//Include style variables
iViz.vue.manage.init();
// Set this to true if want to share virtual study, before user is authenticated
iViz.vue.manage.getInstance().showShareButton = false;
iViz.vue.manage.getInstance().showSaveButton = false;
//Set this to true if want to load user specific cohorts(this is for cbioportal)
iViz.vue.manage.getInstance().loadUserSpecificCohorts = false;
window.cbioURL = 'http://www.cbioportal.org/';
window.appVersion = new Date().getTime();
window.userEmailAddress = '';
window.cbioResourceURL = 'resources/';
window.mutationProfileId = 'acc_tcga_mutations';
window.cnaProfileId = 'acc_tcga_gistic';
window.case_set_id = '-1';
var studyCasesMap = {};
studyCasesMap['acc_tcga'] = {};
window.cohortIdsList = ['acc_tcga'];
window.iviz = {};
window.iviz.datamanager = new DataManagerForIviz.init(window.cbioURL, studyCasesMap);
var getSelectableStudyIds = function() {
var def = new $.Deferred();
$.when(window.iviz.datamanager.getAllPhysicalStudies(),
window.iviz.datamanager.getAllVirtualStudies()).then(function(physicalStudies, virtualStudies) {
var physicalStudyIds = _.pluck(physicalStudies, 'studyId');
var virtualStudyIds = _.pluck(virtualStudies, 'id');
def.resolve(physicalStudyIds.concat(virtualStudyIds))
}).fail(function(error) {
def.reject(error);
});
return def.promise();
};
$.when(window.iviz.datamanager.getConfigs())
.done(function(configs) {
var opts = {};
if (_.isObject(configs)) {
opts = configs;
}
$.when(
window.iviz.datamanager.initialSetup(),
getSelectableStudyIds()
).done(function(_data,selectableIds) {
iViz.init(_data, opts, selectableIds);
}).fail(function(error) {
iViz.vue.manage.getInstance().failedToInit.status = true;
if (error) {
iViz.vue.manage.getInstance().failedToInit.message = error
}
iViz.vue.manage.getInstance().isloading = false;
});
})
.fail(function() {
iViz.vue.manage.getInstance().failedToInit.status = true;
iViz.vue.manage.getInstance().failedToInit.message = 'Failed to load study view configurations.';
iViz.vue.manage.getInstance().isloading = false;
});
QueryByGeneTextArea.init('#query-by-gene-textarea', function(genes) {
iViz.vue.manage.getInstance().$broadcast('gene-list-updated', genes);
});
});
</script>
</html>