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track-picker.html
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track-picker.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Track Picker</title>
<!-- Font Awesome -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/all.min.css">
<!-- Bootstrap 4 CSS -->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.5.1/css/bootstrap.min.css">
<style>
body {
font-family: Arial, sans-serif;
display: flex;
flex-direction: column;
align-items: center;
margin: 20px;
}
h1, h2 {
margin-bottom: 20px;
text-align: center;
}
.table-container {
width: 100%;
margin-bottom: 20px;
overflow-x: auto;
}
table {
width: 100%;
border-collapse: collapse;
margin-bottom: 20px;
table-layout: fixed;
}
th, td {
padding: 8px;
text-align: left;
border: 1px solid #ddd;
box-shadow: 1px 1px 5px rgba(0, 0, 0, 0.1);
overflow: hidden;
white-space: nowrap;
}
th {
background-color: #f2f2f2;
text-align: center; /* Center column headings */
}
.scroll-box {
overflow-x: auto;
white-space: nowrap;
}
.scroll-box td {
width: 150px;
}
.info-box {
width: 100%;
border: 1px solid #ddd;
padding: 8px;
box-sizing: border-box;
margin-bottom: 20px;
white-space: pre-line;
box-shadow: 1px 1px 5px rgba(0, 0, 0, 0.1);
}
.output-box {
width: 100%;
height: 300px; /* Updated height */
overflow: auto;
white-space: pre-wrap;
border: 1px solid #ddd;
padding: 8px;
box-sizing: border-box;
margin-bottom: 20px;
box-shadow: 1px 1px 5px rgba(0, 0, 0, 0.1);
}
footer {
margin-top: 20px;
text-align: center;
padding: 10px;
background-color: #f2f2f2;
border-top: 1px solid #ddd;
width: 100%;
}
.copy-icon {
cursor: pointer;
margin-left: 10px;
font-size: 14px;
color: #007bff;
}
.copy-notification {
display: none;
color: green;
font-size: 12px;
margin-left: 10px;
}
.btn-primary {
background-color: #007bff;
border-color: #007bff;
}
.btn-secondary {
background-color: #6c757d;
border-color: #6c757d;
}
.btn {
margin-bottom: 10px;
}
.file-list {
font-size: 14px;
margin-top: 10px;
text-align: center;
}
.save-notification {
display: none;
color: green;
font-size: 14px;
margin-top: 10px;
}
.centered {
text-align: center;
}
.filename-group {
display: flex;
align-items: center;
justify-content: center;
margin-bottom: 10px;
}
.track-checkbox {
transform: scale(1.2);
display: block;
margin-left: auto;
margin-right: auto;
}
.output-section {
display: flex;
flex-direction: column;
align-items: center;
width: 100%;
}
.select-all {
cursor: pointer;
color: #007bff;
margin-left: 10px; /* Added margin to separate the checkbox from the text */
}
.center-button {
display: flex;
justify-content: center;
width: 100%;
}
.notification-container {
display: flex;
justify-content: center;
width: 100%;
}
.narrow-column {
width: 100px; /* Adjust the width as necessary */
}
</style>
<script src="https://cdnjs.cloudflare.com/ajax/libs/pako/2.0.4/pako.min.js"></script>
</head>
<body>
<h1>Track Picker</h1>
<h2>Load JSON Files</h2>
<label for="jsonFiles" class="btn btn-secondary">
Choose local JSON files...
<input type="file" id="jsonFiles" name="jsonFiles" accept=".json" multiple style="display: none;" onchange="displaySelectedFiles()">
</label>
<div id="fileList" class="file-list"></div>
<div id="blobCount" class="file-list"></div>
<br><br>
<label for="urlInput" class="centered">and/or enter comma-separated URLs or blobs:</label>
<input type="text" id="urlInput" class="form-control" placeholder="Enter URLs or blobs here" style="width: 80%;">
<br><br>
<button class="btn btn-primary" onclick="loadFiles()">Load Files</button>
<h2 id="trackDataHeader" style="display:none;">Track Data</h2>
<div id="tables-container" class="table-container"></div>
<button class="btn btn-primary" id="generateSessionButton" style="display: none;" onclick="generateSessionJson()">Generate Session JSON</button>
<div id="sessionJsonSection" class="output-section" style="display: none;">
<h2>Session JSON Output</h2>
<textarea id="sessionJsonOutput" class="output-box" readonly style="width: 100%;"></textarea>
<br>
<div class="filename-group">
<label for="filenameInput">Filename:</label>
<input type="text" id="filenameInput" class="form-control" value="session.json" style="width: 40%; margin-left: 10px;">
</div>
<div class="center-button">
<button class="btn btn-secondary" id="SaveSessionFile" style="display: inline-block;" onclick="saveSessionFile()">Save Session File</button>
</div>
<div class="notification-container">
<div id="saveNotification" class="save-notification">File saved as: session.json</div>
</div>
</div>
<h2 id="blobUrlHeader" style="display:none;">Blob URL</h2>
<div id="blobUrlOutput" class="centered"></div>
<footer></footer>
<script>
const mode = 'default'; //'secure' or 'default'
let originalData = [];
let trackDataStore = {};
async function loadJSON(url) {
try {
const response = await fetch(url);
if (!response.ok) {
throw new Error(`HTTP error! status: ${response.status}`);
}
return await response.json();
} catch (error) {
console.error(`Failed to fetch JSON from ${url}:`, error);
alert(`Failed to fetch JSON from ${url}: ${error.message}`);
}
}
function readFile(file) {
return new Promise((resolve, reject) => {
const reader = new FileReader();
reader.onload = () => resolve(JSON.parse(reader.result));
reader.onerror = error => reject(error);
reader.readAsText(file);
});
}
async function loadFiles() {
const tablesContainer = document.getElementById('tables-container');
tablesContainer.innerHTML = '';
originalData = [];
trackDataStore = {};
const fileList = document.getElementById('jsonFiles').files;
const enteredURLs = document.getElementById('urlInput').value.split(/,|%2C/).map(url => url.trim()).filter(url => url);
const allPromises = [];
for (const file of fileList) {
allPromises.push(readFile(file));
}
for (const urlOrBlob of enteredURLs) {
const blobPrefix = 'blob:';
const sessionURLPrefix = '?sessionURL=';
if (urlOrBlob.includes(sessionURLPrefix) && urlOrBlob.includes(blobPrefix)) {
const blobContent = urlOrBlob.split(sessionURLPrefix)[1].replace(blobPrefix, '');
allPromises.push(loadBlob(blobContent));
} else if (urlOrBlob.startsWith(blobPrefix)) {
allPromises.push(loadBlob(urlOrBlob.replace(blobPrefix, '')));
} else {
// Convert regular GitHub URLs to raw content URLs
const rawUrl = urlOrBlob.replace('github.com', 'raw.githubusercontent.com').replace('/blob/', '/');
allPromises.push(loadJSON(rawUrl));
}
}
const allData = await Promise.all(allPromises);
originalData = allData.flat().filter(data => data); // Filter out any null or undefined results
originalData.forEach((data, dataIndex) => {
if (data.reference && data.tracks) {
processSessionJSON(data, dataIndex);
} else {
processGenomeJSON(data, dataIndex);
}
});
if (originalData.length > 0) {
document.getElementById('trackDataHeader').style.display = 'block';
document.getElementById('generateSessionButton').style.display = 'inline-block';
}
// Update blob count
const blobCount = enteredURLs.filter(url => url.includes(blobPrefix)).length;
document.getElementById('blobCount').innerText = `Loaded ${blobCount} blob(s)`;
}
function uncompressString(enc) {
enc = enc.replace(/\./g, '+').replace(/_/g, '/').replace(/-/g, '=');
const compressedString = atob(enc);
const compressedBytes = [];
for (let i = 0; i < compressedString.length; i++) {
compressedBytes.push(compressedString.charCodeAt(i));
}
const bytes = pako.inflateRaw(new Uint8Array(compressedBytes));
let str = '';
for (let b of bytes) {
str += String.fromCharCode(b);
}
return str;
}
async function loadBlob(blobContent) {
try {
const decompressedData = uncompressString(blobContent);
return JSON.parse(decompressedData);
} catch (error) {
console.error(`Failed to process blob:`, error);
alert(`Failed to process blob: ${error.message}`);
}
}
function processSessionJSON(data, dataIndex) {
const table = document.createElement('table');
const thead = document.createElement('thead');
thead.innerHTML = `
<tr>
<th>Track Name</th>
<th class="narrow-column">Select<br><input type="checkbox" class="select-all" onclick="toggleSelectAll(this)" style="transform: scale(1.2); margin: 0;"></th>
${mode === 'default' ? '<th>Track URLs</th><th>Index URLs</th><th>Track Data</th>' : ''}
</tr>
`;
table.appendChild(thead);
const tbody = document.createElement('tbody');
// Add reference row
const referenceData = JSON.stringify(data.reference);
const refRow = document.createElement('tr');
refRow.innerHTML = `
<td>Reference</td>
<td></td>
${mode === 'default' ? `
<td class="scroll-box">${data.reference.fastaURL}</td>
<td class="scroll-box">${data.reference.indexURL}</td>
<td class="scroll-box">${referenceData}</td>
` : ''}
`;
tbody.appendChild(refRow);
data.tracks.forEach((track, index) => {
if (track.url) {
const row = document.createElement('tr');
const trackId = `track-${dataIndex}-${index}`;
trackDataStore[trackId] = {
trackURL: track.url || '',
indexURL: track.indexURL || '',
trackData: JSON.stringify(track),
fastaURL: data.reference.fastaURL,
reference: data.reference
};
row.innerHTML = `
<td class="scroll-box">${track.name || track.filename}</td>
<td class="narrow-column"><input type="checkbox" class="track-checkbox" id="${trackId}" style="transform: scale(1.2); margin: auto;"></td>
${mode === 'default' ? `
<td class="scroll-box">${track.url}</td>
<td class="scroll-box">${track.indexURL || ''}</td>
<td class="scroll-box">${JSON.stringify(track)}</td>
` : ''}
`;
tbody.appendChild(row);
}
});
table.appendChild(tbody);
document.getElementById('tables-container').appendChild(table);
}
function processGenomeJSON(genome, dataIndex) {
const table = document.createElement('table');
const thead = document.createElement('thead');
thead.innerHTML = `
<tr>
<th>Track Name</th>
<th class="narrow-column">Select<br><input type="checkbox" class="select-all" onclick="toggleSelectAll(this)" style="transform: scale(1.2); margin: 0;"></th>
${mode === 'default' ? '<th>Track URLs</th><th>Index URLs</th><th>Track Data</th>' : ''}
</tr>
`;
table.appendChild(thead);
const tbody = document.createElement('tbody');
// Add reference row
const referenceData = JSON.stringify({
id: genome.id,
name: genome.name,
fastaURL: genome.fastaURL,
indexURL: genome.indexURL,
cytobandURL: genome.cytobandURL,
aliasURL: genome.aliasURL
});
const refRow = document.createElement('tr');
refRow.innerHTML = `
<td>Reference</td>
<td></td>
${mode === 'default' ? `
<td class="scroll-box">${genome.fastaURL}</td>
<td class="scroll-box">${genome.indexURL}</td>
<td class="scroll-box">${referenceData}</td>
` : ''}
`;
tbody.appendChild(refRow);
genome.tracks.forEach((track, index) => {
const row = document.createElement('tr');
const trackId = `track-${dataIndex}-${index}`;
trackDataStore[trackId] = {
trackURL: track.url || '',
indexURL: track.indexURL || '',
trackData: JSON.stringify(track),
fastaURL: genome.fastaURL,
reference: {
id: genome.id,
name: genome.name,
fastaURL: genome.fastaURL,
indexURL: genome.indexURL,
cytobandURL: genome.cytobandURL,
aliasURL: genome.aliasURL,
chromosomeOrder: genome.chromosomeOrder
}
};
row.innerHTML = `
<td class="scroll-box">${track.name}</td>
<td class="narrow-column"><input type="checkbox" class="track-checkbox" id="${trackId}" style="transform: scale(1.2); margin: auto;"></td>
${mode === 'default' ? `
<td class="scroll-box">${track.url}</td>
<td class="scroll-box">${track.indexURL || ''}</td>
<td class="scroll-box">${JSON.stringify(track)}</td>
` : ''}
`;
tbody.appendChild(row);
});
table.appendChild(tbody);
document.getElementById('tables-container').appendChild(table);
}
function displaySelectedFiles() {
const fileList = document.getElementById('jsonFiles').files;
const fileListDiv = document.getElementById('fileList');
fileListDiv.innerHTML = '';
for (const file of fileList) {
const fileItem = document.createElement('div');
fileItem.textContent = file.name;
fileListDiv.appendChild(fileItem);
}
}
function compressString(str) {
const bytes = new Uint8Array(str.length);
for (let i = 0; i < str.length; i++) {
bytes[i] = str.charCodeAt(i);
}
const compressedBytes = pako.deflateRaw(bytes);
const compressedString = String.fromCharCode.apply(null, compressedBytes);
let enc = btoa(compressedString);
return enc.replace(/\+/g, '.').replace(/\//g, '_').replace(/=/g, '-');
}
function generateSessionJson() {
console.log('Generate Session JSON button clicked');
const checkboxes = document.querySelectorAll('.track-checkbox:checked');
console.log('Selected checkboxes:', checkboxes);
const selectedTracks = Array.from(checkboxes).map(checkbox => {
const trackId = checkbox.id;
console.log('Selected track ID:', trackId);
return JSON.parse(trackDataStore[trackId].trackData);
});
if (selectedTracks.length === 0) {
alert('No tracks selected.');
return;
}
const uniqueFastaURLs = new Set();
const trackGroups = {};
checkboxes.forEach(checkbox => {
const trackId = checkbox.id;
const { trackURL, fastaURL, reference } = trackDataStore[trackId];
uniqueFastaURLs.add(fastaURL);
if (!trackGroups[trackURL]) {
trackGroups[trackURL] = [];
}
trackGroups[trackURL].push(JSON.parse(trackDataStore[trackId].trackData));
// Ensure reference is set correctly
if (uniqueFastaURLs.size === 1) {
selectedReference = reference;
}
});
if (uniqueFastaURLs.size > 1) {
alert('Tracks from different references cannot be combined.');
return;
}
if (!selectedReference) {
alert('Reference not found for the selected tracks.');
return;
}
const sessionJson = {
version: "2.15.11",
showSampleNames: false,
reference: selectedReference,
locus: "all",
roi: [],
tracks: Object.values(trackGroups).flat()
};
if (mode === 'default') {
document.getElementById('sessionJsonOutput').textContent = JSON.stringify(sessionJson, null, 2);
document.getElementById('sessionJsonSection').style.display = 'block';
}
// Generate blob URL from session JSON
const compressedString = compressString(JSON.stringify(sessionJson));
const blobUrl = `https://ink-blot.github.io/?sessionURL=blob:${compressedString}`;
document.getElementById('blobUrlOutput').innerHTML = `<a href="${blobUrl}" target="_blank">Click link</a> <i class="fas fa-copy copy-icon" onclick="copyToClipboard('${blobUrl}')"></i>`;
document.getElementById('blobUrlHeader').style.display = 'block';
}
function toggleSelectAll(selectAllCheckbox) {
const checkboxes = document.querySelectorAll('.track-checkbox');
checkboxes.forEach(checkbox => {
checkbox.checked = selectAllCheckbox.checked;
});
}
function saveSessionFile() {
const blob = new Blob([document.getElementById('sessionJsonOutput').value], { type: 'application/json' });
const url = URL.createObjectURL(blob);
const a = document.createElement('a');
a.href = url;
a.download = document.getElementById('filenameInput').value || 'session.json';
document.body.appendChild(a);
a.click();
document.body.removeChild(a);
// Show save notification
const saveNotification = document.getElementById('saveNotification');
saveNotification.style.display = 'block';
setTimeout(() => {
saveNotification.style.display = 'none';
}, 2000); // Hide notification after 2 seconds
}
function copyToClipboard(text) {
const textarea = document.createElement('textarea');
textarea.value = text;
document.body.appendChild(textarea);
textarea.select();
document.execCommand('copy');
document.body.removeChild(textarea);
// Show copy notification
const copyNotification = document.createElement('div');
copyNotification.textContent = 'Copied!';
copyNotification.style.color = 'green';
copyNotification.style.fontSize = '14px';
copyNotification.style.marginLeft = '10px';
document.getElementById('blobUrlOutput').appendChild(copyNotification);
setTimeout(() => {
document.getElementById('blobUrlOutput').removeChild(copyNotification);
}, 2000); // Hide notification after 2 seconds
}
// Automatically load files if sessionURL parameter is present in the URL
window.onload = async function() {
const urlParams = new URLSearchParams(window.location.search);
const sessionURLs = urlParams.get('sessionURL');
if (sessionURLs) {
const processedURLs = sessionURLs.split(/,|%2C/).map(url => url.trim());
document.getElementById('urlInput').value = processedURLs.join(', ');
await loadFiles();
}
}
</script>
</body>
</html>