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main_page_template.html
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<!DOCTYPE html>
<html>
<head>
<title>Broad COVID-19 Testing Dashboard</title>
<link rel="icon" type="image/x-icon" href="static/favicon.ico">
<meta name="description" content="Statistics on COVID-19 testing at the Broad Institute of MIT and Harvard in Cambridge, MA, USA.">
<meta name="viewport" content="width=device-width, initial-scale=1">
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/css/bootstrap.min.css" integrity="sha384-Vkoo8x4CGsO3+Hhxv8T/Q5PaXtkKtu6ug5TOeNV6gBiFeWPGFN9MuhOf23Q9Ifjh" crossorigin="anonymous">
<meta http-equiv="refresh" content="600">
<style type="text/css">
body, wrapper {
min-height: 100vh;
}
nav {
background-color: #FAFBFC;
border-bottom: 1px solid rgba(72, 94, 144, 0.16);
}
.card-title {
text-transform: uppercase;
font-size: 14px;
letter-spacing: 0.5px;
color: #1b2e4b;
font-weight: 600;
}
.card-main-info {
color: rgb(33, 37, 41);
display: inline-block;
font-size: 28px;
font-weight: 500;
margin: 0px 8px 8px 0px;
text-align: left;
/* min-width: 85px; */
}
.card-main-info-samples-from {
color: rgb(33, 37, 41);
display: inline-block;
font-size: 20px;
font-weight: 500;
margin: 0px 5px 8px 0px;
text-align:left;
/* min-width:65px; */
}
.card-secondary-info {
color: rgb(33, 37, 41);
display: inline-block;
font-size: 15px;
font-weight: 500;
text-align:left;
}
.card-small-text {
color: rgb(33, 37, 41);
display: inline-block;
font-size: 13px;
font-weight: 500;
text-align:left;
}
footer {
border-top: 1px solid rgba(72, 94, 144, 0.16);
background-color: #FAFBFC;
}
.section-title {
font-size: 22px;
font-weight: bolder;
font-weight: 500;
}
@media (min-width: 1400px) {
.no-padding-right-in-large-screens {
padding-right:0px !important;
}
.col-xl-3-and-a-half {
width: 28%;
flex: 0 0 28%;
max-width: 28%;
}
.col-xl-8-and-a-half {
width: 72%;
flex: 0 0 72%;
max-width: 72%;
}
}
@media only screen and (max-width: 1400px) {
.expands-in-small-screens {
flex: 0 0 100% !important;
max-width: 100% !important;
}
.hide-in-small-screen {
display: none;
}
}
</style>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=UA-161539452-1"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'UA-161539452-1');
</script>
</head>
<body>
<wrapper class="d-flex flex-column">
<nav class="navbar navbar-default navbar-static-top">
<div class="container">
<div class="row flex-fill">
<div class="col-sm-3 text-center">
<a class="navbar-brand" href="https://www.broadinstitute.org/" style="margin: 3px 10px 3px 0px">
<img src="static/BroadInstLogoforDigitalRGB.png" width="170" height="43" />
</a>
</div>
<div class="col-sm-12 col-lg-9 text-center" style="align-self: center; font-size: 27px; font-family: sans-serif; font-weight: 300">
COVID-19 Diagnostic Processing Dashboard
</div>
</div>
</div>
</nav>
<div class="content content-fixed flex-fill">
<div class="container">
<div class="row">
<div class="col-lg-0 col-sm-0"></div>
<div class="col-sm-12 col-lg-12 mt-4 mb-5 expands-in-small-screens">
In late March 2020, Broad Institute <a href="https://www.broadinstitute.org/news/how-broad-institute-converted-clinical-processing-lab-large-scale-covid-19-testing-facility">rapidly converted our large-scale genomics facility</a> into a center that can process SARS-CoV-2 tests. Working in partnership with the Commonwealth of Massachusetts, Massachusetts State Public Health Laboratory, and medical facilities in the Commonwealth, the Broad's CLIA-certified lab processes samples collected from patients in Massachusetts and beyond.<br />
<br />
This page shows the number of SARS-CoV-2 viral diagnostic and surveillance tests processed at the Clinical Research Sequencing Platform (CRSP) at the Broad Institute of MIT and Harvard.<br />
<br />
These numbers are updated during the course of the day as samples are completed at Broad. For details on the testing program, visit the <a href="https://www.broadinstitute.org/covid-19-testing">Broad Institute website</a>.<br/>
</div>
</div>
<div class="row">
<div class="col-lg-3 col-xl-3-and-a-half expands-in-small-screens no-padding-right-in-large-screens" style="padding-bottom: 2rem;">
<div class="card card-body mt-2" style="background-color: #FFFFFF">
<h6 class="card-title">
<span style="color:#439798">Total</span> Tests Completed
</h6>
<div style="white-space: nowrap">
<h3 class="card-main-info" style="color:#439798">{{TOTAL_COMPLETED}}</h3>
<span class="card-secondary-info"> since 3/25/2020</span>
</div>
</div>
<div class="card card-body mt-2" style="background-color: #FFFFFF">
<h6 class="card-title">
<span style="color:#e18b50">Positive </span>Tests
</h6>
<div style="white-space: nowrap">
<h3 class="card-main-info" style="color:#e18b50">{{TOTAL_POSITIVE}}</h3>
<div><span class="card-main-info">{{TOTAL_POSITIVE_PERCENT}}%</span> of tests</div>
<div><span id="rolling-ave" class="card-main-info"></span><span class="card-small-text"> last 7-day rolling average</span></div>
</div>
</div>
<div class="card card-body mt-2" style="background-color: #FFFFFF">
<h7 class="card-title">
<span style="color: gray;">Inconclusive & Invalid </span>Tests
<a target="_blank" href="https://covid-19-test-info.broadinstitute.org/#unsatisfactory-tnp-test-not-performed-result-code-information" style="padding-left: 1px; text-decoration: none; color: #AAAAAA">
<i class="fa fa-question-circle-o" target="_blank"></i>
</a>
</h7>
<div style="white-space: nowrap">
<h3 class="card-main-info" style="color: gray;">{{TOTAL_INCONCLUSIVE}}</h3>
<div><span class="card-main-info">{{TOTAL_INCONCLUSIVE_PERCENT}}%</span> of tests</div>
</div>
</div>
<div class="card card-body mt-2" style="background-color: #FFFFFF; display: none;">
<h7 class="card-title">
Tests by Region
</h7>
<div style="white-space: nowrap">
<h3 class="card-main-info-samples-from">{{TOTAL_FROM_MA}}</h3>
<span class="card-secondary-info" style="color:gray"> from MA </span>
<span class="card-secondary-info">({{TOTAL_FROM_MA_PERCENT}}%)</span>
<br />
<h3 class="card-main-info-samples-from">{{TOTAL_FROM_OUT_OF_STATE}}</h3>
<span class="card-secondary-info" style="color:gray"> from out of state </span>
<span class="card-secondary-info">({{TOTAL_FROM_OUT_OF_STATE_PERCENT}}%)</span>
</div>
</div>
</div><!-- col -->
<div class="col-lg-12 col-xl-8-and-a-half mt-2">
<div class="btn-group btn-group-sm" role="group" aria-label="time scales" style="width: 100%; padding-bottom: 2rem;">
<button type="button" class="btn btn-outline-secondary">1W</button>
<button type="button" class="btn btn-outline-secondary">1M</button>
<button type="button" class="btn btn-outline-secondary active">3M</button>
<button type="button" class="btn btn-outline-secondary">6M</button>
<button type="button" class="btn btn-outline-secondary">All</button>
</div>
<div>
<figure class="highcharts-figure">
<div id="chart-1"></div>
</figure>
<hr style="border-top: 5px solid #eeeeee">
<figure class="highcharts-figure">
<div id="chart-2"></div>
</figure>
<hr style="border-top: 5px solid #eeeeee">
<figure class="highcharts-figure">
<div id="chart-3"></div>
</figure>
<hr style="border-top: 5px solid #eeeeee; border-bottom: 5px solid #eeeeee">
<figure class="highcharts-figure">
<div id="chart-4"><!--pooled sample daily volume--></div>
</figure>
<hr style="border-top: 5px solid #eeeeee">
<figure class="highcharts-figure">
<div id="chart-6"></div>
</figure>
<hr style="border-top: 5px solid #eeeeee">
</div>
<div class="text-secondary mt-5" style="margin:50px 10px">
The numbers will not match the daily reports from the State of Massachusetts for several reasons:
<ul>
<li>Some people are tested more than once (for example, as a confirmation or re-test, or as part of an ongoing college/university testing program). The figures here reflect the number of tests performed, not the number of people tested.</li>
<li>Broad Institute processes some tests from other states.</li>
</ul>
The "percent positive" pertains to the tests submitted to Broad. Because different organizations use different criteria for selecting individuals for testing, it is not possible to draw meaningful conclusions about infection rates or trends from these data. <br />
<br />
The Clinical Research Sequencing Platform, LLC is a subsidiary of the Broad Institute.<br />
</div>
</div>
</div><!-- row -->
</div><!-- container -->
</div>
<footer>
<div class="container text-right" style="padding:10px">
<span style="font-size: 15px; padding-right: 20px">
<a href="mailto:[email protected]" style="text-decoration:none; font-weight:500">
<span style="padding-left: 10px">Contact Us</span>
<i class="fa fa-envelope" aria-hidden="true" style="padding-left: 35px"></i>
</a>
<a target="_blank" href="https://twitter.com/broadinstitute" style="text-decoration: none; margin-left: 7px">
<i class="fa fa-twitter" aria-hidden="true"></i>
</a>
<a target="_blank" href="https://github.com/broadinstitute/covid19-testing/issues" style="text-decoration: none; margin-left: 7px">
<i class="fa fa-github" aria-hidden="true"></i>
</a>
</span>
</div>
</footer>
</wrapper>
</body>
<script src="https://code.highcharts.com/highcharts.js"></script>
<script src="https://code.highcharts.com/modules/exporting.js"></script>
<script src="https://code.highcharts.com/modules/export-data.js"></script>
<script src="https://code.highcharts.com/modules/accessibility.js"></script>
<script src="https://code.highcharts.com/modules/pattern-fill.js"></script>
<script src="https://code.jquery.com/jquery-3.4.1.slim.min.js" integrity="sha384-J6qa4849blE2+poT4WnyKhv5vZF5SrPo0iEjwBvKU7imGFAV0wwj1yYfoRSJoZ+n" crossorigin="anonymous"></script>
<script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/umd/popper.min.js" integrity="sha384-Q6E9RHvbIyZFJoft+2mJbHaEWldlvI9IOYy5n3zV9zzTtmI3UksdQRVvoxMfooAo" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.4.1/js/bootstrap.min.js" integrity="sha384-wfSDF2E50Y2D1uUdj0O3uMBJnjuUD4Ih7YwaYd1iqfktj0Uod8GCExl3Og8ifwB6" crossorigin="anonymous"></script>
<script>
//docs @ https://api.highcharts.com/highcharts/
let data = {{DATA|tojson}};
// let currentTime = new Date(new Date().toLocaleDateString());
let currentTime = new Date(new Date().toLocaleDateString('en-US'));
configFigureMenu();
setChartGlobalConfig();
render("All");
function configFigureMenu(){
let tScale = null;
$(".btn-group > button.btn").on("click", function() {
$(".btn-group > button.btn").removeClass("active");
$(this).addClass("active");
tScale = this.innerHTML;
console.log("time scale is " + tScale);
render(tScale);
})
}
function setChartGlobalConfig() {
Highcharts.setOptions({
credits: {
enabled: false
},
lang: {
thousandsSep: ','
},
chart: {
marginRight: 20,
time: {
timezone: 'America/New_York'
},
},
xAxis: {
type: 'datetime',
crosshair: true,
startOnTick: true,
tickInterval: 7 * 24 * 3600 * 1000,
labels: {
rotation: 60,
formatter() {
return Highcharts.dateFormat('%b-%e', this.value)
}
},
min: undefined
},
responsive: {
rules: [{
condition: {
maxWidth: 700,
},
chartOptions: {
yAxis: {
minorTicks: true,
}
}
}]
}
})
}
function render(tScale) {
let interval = null;
switch(tScale){
case "1W":
interval = 6.048*1e8;
break;
case "1M":
interval = 2.628*1e9;
break;
case "3M":
interval = 7.884*1e9;
break;
case "6M":
interval = 1.577*1e10;
break;
default:
interval = undefined;
}
let tMin = interval===undefined?undefined:currentTime.getTime() - interval;
let xAxis = {
type: 'datetime',
crosshair: true,
tickInterval: tScale=="1W"?24*3600*1000:7*24*3600*1000,
startOnTick: false,
labels: {
rotation: 60,
formatter() {
return Highcharts.dateFormat('%b-%e', this.value)
}
},
min: tMin
};
plotCumulativeTests(xAxis);
plotDailyVolume(xAxis);
plotDailyPositiveRate(xAxis);
plotPooledDailyVolume(xAxis);
plotPooledDailyPositiveRate(xAxis);
}
function plotCumulativeTests(xAxis) {
const cumulativeTotals = []
data.reduce(function(a, x, i) {
let v = a + x.positive + x.negative + x.inconclusive;
let time = new Date(x.day.replace(/-/g, "/")).getTime();
cumulativeTotals[i] = [time, v];
return v;
}, 0);
const cumulativePositives = [];
data.reduce(function(a, x, i) {
let v = a + x.positive;
let time = new Date(x.day.replace(/-/g, "/")).getTime();
cumulativePositives[i] = [time, v];
return v
}, 0)
Highcharts.chart('chart-1', {
chart: {
type: 'spline',
height: '350px',
},
time: {
useUTC: false
},
legend: {
floating: true,
align: 'left',
verticalAlign: 'top',
layout: 'vertical',
x: 60,
y: 30,
backgroundColor: '#ffffff'
},
title: {
text: 'Cumulative Volume'
},
plotOptions: {
series: {
dataLabels: {
enabled: false,
y: -5,
},
}
},
tooltip: {
headerFormat: '<span style="font-size:10px">{point.key}</span><table>',
pointFormat: '<tr><td style="color:{series.color}">{series.name}: </td><td style="padding-left: 5px"><b>{point.y:,.0f}</b></td></tr>',
footerFormat: '</table>',
shared: true,
useHTML: true
},
xAxis: xAxis,
yAxis: {
tickAmount: 5,
min: 0,
title: {
enabled: false,
},
},
series: [
{
name: 'Cumulative Tests Completed',
data: cumulativeTotals,
color: "#439798", //"#00AA00AA",
}, {
name: 'Cumulative Positives',
data: cumulativePositives,
color: "#e18b50", //"#BB0000AA",
}]
});
}
function plotDailyVolume(xAxis) {
Highcharts.chart('chart-2', {
global: {
useUTC: false
},
chart: {
height: '350px',
},
legend: {
floating: true,
align: 'left',
verticalAlign: 'top',
layout: 'vertical',
x: 60,
y: 30,
backgroundColor: '#ffffff'
},
title: {
text: 'Daily Volume'
},
plotOptions: {
column: {
stacking: 'normal',
pointPadding: 0.2,
borderColor: '#439798',
borderWidth: 1,
},
},
tooltip: {
headerFormat: '<span style="font-size:10px">{point.key}</span><table>',
pointFormat: '<tr><td style="color:{series.color}">{series.name}: </td><td style="padding-left: 5px;min-width:60px;"><b>{point.y:,.0f}</b></td></tr>',
footerFormat: '</table>',
shared: true,
useHTML: true
},
xAxis: xAxis,
yAxis: {
reversedStacks: false,
min: 0,
tickInterval: 20000,
title: {
enabled: false,
}
},
series: [
{
name: 'Tests Completed',
type: 'column',
data: data.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
return [time, x.positive + x.negative + x.inconclusive];
}),
color: "#439798", //"#00AA00AA",
dataLabels: {
enabled: false,
},
},
]
}, function(chart) {
var series = chart.series;
$.each(series, function(i, ser) {
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$(ser.legendSymbol.element).attr('stroke','#439798');
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}
function plotPooledDailyVolume(xAxis) {
Highcharts.chart('chart-4', {
global: {
useUTC: false
},
chart: {
height: '250px',
},
legend: {
floating: true,
align: 'left',
verticalAlign: 'top',
layout: 'vertical',
x: 60,
y: 30,
backgroundColor: '#ffffff'
},
title: {
text: 'Pooled Tests Daily Volume'
},
plotOptions: {
column: {
borderColor: '#439798',
borderWidth: 0,
grouping: false,
shadow: false
}
},
tooltip: {
headerFormat: '<span style="font-size:10px">{point.key}</span><table>',
pointFormat: '<tr><td style="color:{series.color}">{series.name}: </td>' +
'<td style="padding-left: 5px;min-width:60px;"><b>{point.y:,.0f}</b></td>' +
'</tr>',
footerFormat: '</table>',
shared: true,
useHTML: true
},
xAxis: xAxis,
yAxis: {
reversedStacks: false,
min: 0,
softMax: 2000,
tickInterval: 500,
title: {
enabled: false,
}
},
series: [
{
name: 'Pooled Samples',
type: 'column',
data: data.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
return [time, x.samplesPooled];
}),
color: "rgb(67, 122, 152, 0.5)", //"#00AA00AA",
dataLabels: {
enabled: false,
},
pointPadding: 0,
},
{
name: 'Individuals',
type: 'column',
data: data.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
return [time, x.individualsPooled];
}),
color: "rgb(67, 122, 152)", //"#00AA00AA",
dataLabels: {
enabled: false,
},
pointPadding: 0.4,
pointPlacement: 0.3
},
]
}, function(chart) {
var series = chart.series;
$.each(series, function(i, ser) {
$(ser.legendSymbol.element).attr('stroke-width','1');
$(ser.legendSymbol.element).attr('stroke','#439798');
});
});
}
function plotDailyPositiveRate(xAxis) {
// calculate the 7-day rolling average
const dataReverse = [...data].reverse();
let rollingAve = []; // assumption: the array, data, is sorted by date and without missing days
dataReverse.forEach( function(x, i) {
let j = i + 7;
if (j<dataReverse.length){
let week = dataReverse.slice(i, j);
let totalPositive = week.reduce(function(a, d){
a = a + d.positive;
return a;
}, 0);
let totalTest = week.reduce(function(a, d){
a = a + d.inconclusive+d.negative+d.positive;
return a;
}, 0);
rollingAve.unshift({
day: x.day,
positive: totalPositive,
total: totalTest
})
}
});
// report the most recent rolling ave in the left-side report card
const mostRecent = rollingAve[rollingAve.length-1];
$("#rolling-ave").text(`${(100 * (mostRecent.positive/mostRecent.total)).toFixed(2)}%`);
// rendering
Highcharts.chart('chart-3', {
chart: {
height: '300px',
},
legend: {
floating: true,
align: 'left',
verticalAlign: 'top',
layout: 'vertical',
x: 60,
y: 20,
backgroundColor: '#ffffff'
},
title: {
text: 'Daily Positive Rate'
},
plotOptions: {
column: {
borderWidth: 0,
},
series: {
marker: {
enabled: false
}
}
},
xAxis: xAxis,
yAxis: [
{
endOnTick: false,
min: 0,
// max: 40,
softMax: 5,
tickAmount: 5,
title: {
enabled: false,
},
labels: {
format: "{value} %",
}
}
],
tooltip: {
valueDecimals: 2,
valueSuffix: '',
headerFormat: '<span style="font-size:10px">{point.key}</span><table>',
pointFormat: '<tr><td style="color:{series.color}">{series.name}: </td><td style="padding-left: 5px;min-width:60px;"><b>{point.display}</b></td></tr>',
footerFormat: '</table>',
shared: true,
useHTML: true
},
series: [
{
name: '% Positive (7-day Rolling Average)',
type: 'line',
data: rollingAve.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
// return [time, 100 * x.positive/x.total, x.positive]
return {
x: time,
y: 100 * x.positive/x.total,
display: (100 * x.positive/x.total).toPrecision(3) + "%"
}
}),
color: "#aaaaaa",
lineWidth: 3
},
{
name: '% Positive (Daily)',
type: 'line',
data: data.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
return {
x: time,
y: 100 * x.positive/(x.positive + x.negative + x.inconclusive),
display: (100 * x.positive/(x.positive + x.negative + x.inconclusive)).toPrecision(3) + "% " + `(${x.positive}/${x.positive + x.negative + x.inconclusive})`
}
}),
color: "#e18b50", //"#BB0000AA",
lineWidth: 2
}
]
});
}
function plotPooledDailyPositiveRate(xAxis) {
// rendering
Highcharts.chart('chart-6', {
chart: {
height: '300px',
},
legend: {
floating: true,
align: 'left',
verticalAlign: 'top',
layout: 'vertical',
x: 60,
y: 20,
backgroundColor: '#ffffff'
},
title: {
text: 'Daily Positive Rate from Pooled Samples'
},
plotOptions: {
column: {
borderWidth: 0,
},
series: {
marker: {
enabled: false
}
}
},
xAxis: xAxis,
yAxis: [
{
endOnTick: false,
min: 0,
softMax: 5,
tickAmount: 5,
title: {
enabled: false,
},
labels: {
format: "{value} %",
}
}
],
tooltip: {
valueDecimals: 2,
valueSuffix: '%',
headerFormat: '<span style="font-size:10px">{point.key}</span><table>',
pointFormat: '<tr><td style="color:{series.color}">{series.name}: </td><td style="padding-left: 5px;min-width:60px;"><b>{point.y}</b></td></tr>',
footerFormat: '</table>',
shared: true,
useHTML: true
},
series: [
{
name: '% Positive (pooled positives/samples)',
type: 'line',
data: data.map(function(x) {
const time = new Date(x.day.replace(/,/g, '/')).getTime();
return [time, 100 * (x.poolPositives/x.samplesPooled)]
}),
color: "#9f64a1",
lineWidth: 1
}
]
});
}
</script>
</html>