9f8d33c8b2b6bc61f6d02d781c4e02836f7099f9
max
Fri Aug 21 02:05:42 2026 -0700
hgSession: new opt-in JavaScript "My Sessions" page; share gbModern.css with hgBlat. refs #38157
Applies the hgBlat facelift strategy (#37996) to hgSession: an opt-in,
client-rendered "My Sessions" page gated by the sessionNewPage /
sessionNewPageBanner hg.conf flags (mirroring blatNewForm / blatNewFormBanner),
with a banner linking between the classic and new pages so neither is a one-way
door. sessionNewPage also flips the site default.
hgSession.c stays the data/action backend: it emits the session list and page
config as an inline JSON global (hgSessionData) into an empty #sessionApp
container, and the new hgSession.js builds the UI - a save-current-view card
(name + optional description + "only I can load it"; empty name saves under a
random share_ name), a "most recently saved session" one-click Update, a
searchable/sortable/paged DataTable of sessions (assembly + position, created
with last-used on hover, views, a lock icon on private sessions), inline Share
(copy link / email / gallery), Edit (rename + description + private), Overwrite
and Delete, and a bulk Select -> Delete-all-selected mode. The mutating actions
POST to new JSON endpoints (hgS_doDeleteJson / doShareJson / doGalleryJson /
doOverwriteJson / doDescribeJson) that run the same SQL as the classic full-page
handlers and return JSON, so the table updates in place; loads, file up/downloads
and custom-track backup stay as ordinary form submits/links. The Advanced panel
keeps feature parity with the classic page (load another user's session, load
from URL/file, save to file, back up custom tracks, reset), minus the login/
change-password links that now live in the top menu.
Shared UCSC house-style components (design tokens, .gbPill, .gbCard, .gbStrip,
.gbSection, .gbShareBox, .gbBanner, the .gbModal* dialog and a .gbTable) are
factored into a new gbModern.css. hgBlat is migrated onto it: its generic
.blat* classes are renamed to the shared .gb* names in hgBlat.css / hgBlat.js
and the #blatResults / #blatFormBox containers get class="gbApp"; verified
pixel-clean against the previous search form and results pages, including the
rename modal. hgSession.css holds only session-specific layout.
diff --git src/hg/js/hgBlat.js src/hg/js/hgBlat.js
index d3f66718551..aae33b07a69 100644
--- src/hg/js/hgBlat.js
+++ src/hg/js/hgBlat.js
@@ -1,899 +1,899 @@
// hgBlat.js - client-side rendering of the hgBlat "Table" output mode.
//
// hgBlat.c emits an inline object var hgBlatData = { config, hits } and an empty
//
. This script builds the whole results UI from that data:
// - a card with a summary strip (query / length / assembly / hit count + actions)
// - a sortable, filterable DataTable whose cells are rendered here (identity bar,
// query-coverage bar, linked loci, action links, comma-formatted position)
// - a docked "selected hit" detail panel updated on row click
// Header tooltips reuse the Genome Browser's own mechanism (title + convertTitleTagsToMouseovers).
/* jshint esnext: true */
/* global $, hgBlatData, convertTitleTagsToMouseovers, htmlEncode */
var blatSelectedRank = null; // rank of the row shown in the detail panel
function blatFmt(n) {
// 12345 -> "12,345"
return Number(n).toLocaleString('en-US');
}
function blatIdColor(id) {
// UCSC identity semantic colors
if (id >= 98) { return '#1f7a34'; }
if (id >= 95) { return '#4d7c0f'; }
if (id >= 90) { return '#b45309'; }
return '#b1301f';
}
// ---- cell renderers ------------------------------------------------------
function blatPositionCell(hit) {
// For alt/fix/random/chrUn sequences show an info icon linking to the FAQ ("What is chr_alt &
// chr_fix?"), with the short explanation as its tooltip. (Sits after the position link, not
// nested inside it.)
var note = hit.chromNote ?
` ⓘ` : '';
// The position links to the Genome Browser at this match; the new-tab icon right after it opens
// the same in a new tab (whitespace between them, no divider).
// URLs are htmlEncode'd before going into href="": they can carry the user's query name, so an
// unescaped double-quote would otherwise break out of the attribute (XSS).
return `${htmlEncode(hit.chrom)}:` +
`${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}` +
` ${note}`;
}
function blatActionsCell(hit) {
// The "Open" column now holds just the base-by-base alignment link (Browser moved to the Position
// column). detailsUrl is htcUserAli on a fresh search, htcBlatAlign on a shared-link reopen; guard
// in case a future caller omits it.
if (!hit.detailsUrl) { return ''; }
// htmlEncode the URL: detailsUrl embeds the user's query name, so an unescaped quote could break
// out of the href attribute (XSS).
return `Alignment`;
}
function blatLocusCell(hit) {
// Locus is plain text (not a link): the gene names are shown for context only. The cell grows with
// its content up to a max-width, then a very long locus (many overlapping genes) is clipped with a
// CSS ellipsis; the full string is always available on mouseover (title).
if (!hit.locusText) { return ''; }
return `
${htmlEncode(hit.locusText)}
`;
}
function blatScoreCell(hit, maxScore) {
// Score with a little bar chart after it, scaled to the highest score in this result set.
var pct = maxScore > 0 ? (hit.score / maxScore * 100) : 0;
return `${blatFmt(hit.score)}` +
``;
}
function blatIdentityCell(hit) {
// Just the percentage now (the bar chart moved to the Score column), kept in its semantic color.
var c = blatIdColor(hit.identity);
return `${hit.identity.toFixed(1)}%`;
}
function blatCoverageCell(hit) {
var left = (hit.qStart - 1) / hit.qSize * 100;
var width = (hit.qEnd - hit.qStart + 1) / hit.qSize * 100;
var tip = `Query matches the genome at ${blatFmt(hit.qStart)}-${blatFmt(hit.qEnd)}bp out of ${blatFmt(hit.qSize)}bp`;
return ``;
}
// ---- summary strip + detail panel ---------------------------------------
function blatSummaryStrip(cfg, queryCount) {
- var stat = (k, v) => `
${k}` +
+ var stat = (k, v) => `
${k}` +
`${v}
`;
- var div = '';
+ var div = '';
var assembly = stat('Assembly', htmlEncode(cfg.organism) + ' / ' + htmlEncode(cfg.db)) + div +
stat('Matches', blatFmt(cfg.hitCount));
var stats;
if (cfg.multiQuery) {
// With more than one query sequence a single query name/length would be wrong, so show the
// number of distinct queries; each hit's own query is in the table's Query column.
stats = stat('Queries', blatFmt(queryCount)) + div + assembly;
} else {
stats = stat('Query', htmlEncode(cfg.queryName)) + div +
stat('Length', blatFmt(cfg.querySize) + ' bp') + div + assembly;
}
var actions = '';
// "View all in browser" is the primary action, so it comes first.
if (cfg.viewAllUrl) {
- actions += `View all in browser`;
+ actions += `View all in browser`;
}
// "Show Query Sequence" opens the query FASTA in a panel (with Download / Copy). Only on a fresh
// search, where the uploaded sequence is available (cfg.querySeqs emitted by hgBlat.c).
if (cfg.querySeqs && cfg.querySeqs.length) {
- actions += '';
}
// "Share a link" just reveals the page's stable URL (cfg.shareUrl, a trash-backed reopen link).
// cfg.canShare covers old session-based links (?u=&s=), where the current URL is already shareable.
if (cfg.shareUrl || cfg.canShare) {
// A small share-nodes icon precedes the label so users learn to associate it with sharing.
var shareIcon = '';
- actions += '';
}
// "Rename BLAT Track" opens a modal to rename the results custom track. This is a JS-native
// button (renders immediately with the strip) that replaces the old C-emitted inline form, which
// only appeared after the buildBigPsl AJAX finished and reflowed the page when clicked.
if (cfg.canRename) {
- actions += '';
}
- return `
${stats}${actions}
`;
+ return `
${stats}${actions}
`;
}
var BLAT_TILE_TIPS = {
'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.',
'Identity': 'Percent identity of the aligned bases.',
'Matches': 'Query bases that match the genome.',
'Mismatch': 'Bases that differ between query and genome.',
'Gaps': 'Number of gaps (insertions or deletions) in the alignment.',
'Blocks': 'Number of ungapped aligned blocks.',
'Strand': 'Genome strand the query matched (+ or -).',
'Q span': 'Range of the query sequence that aligned (1-based).'
};
function blatTileSkeleton(label, id, color) {
var style = color ? ` style="color:${color}"` : '';
var tip = BLAT_TILE_TIPS[label] || '';
return `
${label}
` +
`
`;
}
function blatDetailSkeleton() {
// Built once; blatRenderDetail() only updates values, so the tile-label tooltips
// are wired a single time by convertTitleTagsToMouseovers.
var tiles =
blatTileSkeleton('Score', 'dvScore') +
blatTileSkeleton('Identity', 'dvIdentity') +
blatTileSkeleton('Matches', 'dvMatches') +
blatTileSkeleton('Mismatch', 'dvMismatch') +
blatTileSkeleton('Gaps', 'dvGaps') +
blatTileSkeleton('Blocks', 'dvBlocks') +
blatTileSkeleton('Strand', 'dvStrand') +
blatTileSkeleton('Q span', 'dvQspan');
document.getElementById('blatDetail').innerHTML =
`
`;
if (typeof convertTitleTagsToMouseovers === 'function') { convertTitleTagsToMouseovers(); }
}
function blatSet(id, prop, val) {
var e = document.getElementById(id);
if (!e) { return; }
if (prop === 'text') { e.textContent = val; }
else if (prop === 'href') { e.setAttribute('href', val); }
else if (prop === 'color') { e.style.color = val; }
}
function blatRenderDetail(hit) {
if (!hit || !document.getElementById('blatDetail')) { return; }
if (!document.getElementById('dvScore')) { blatDetailSkeleton(); }
var idc = blatIdColor(hit.identity);
// Location line is plain text, so set it via textContent (blatSet 'text') - no HTML, nothing to
// escape. q and locus stay raw here for that reason.
var locus = hit.locusText ? hit.locusText + ' · ' : '';
var q = hgBlatData.config.multiQuery ? hit.qName + ' · ' : '';
blatSet('dvLoc', 'text',
`#${hit.rank} · ${q}${locus}${hit.chrom}:${blatFmt(hit.tStart)}-${blatFmt(hit.tEnd)}`);
blatSet('dvScore', 'text', blatFmt(hit.score));
blatSet('dvIdentity', 'text', hit.identity.toFixed(1) + '%');
blatSet('dvIdentity', 'color', idc);
blatSet('dvMatches', 'text', blatFmt(hit.matches));
blatSet('dvMismatch', 'text', blatFmt(hit.misMatch));
blatSet('dvGaps', 'text', blatFmt(hit.gaps));
blatSet('dvBlocks', 'text', blatFmt(hit.blocks));
blatSet('dvStrand', 'text', hit.strand);
blatSet('dvQspan', 'text', blatFmt(hit.qStart) + '–' + blatFmt(hit.qEnd));
blatSet('dvBrowser', 'href', hit.browserUrl);
blatSet('dvNewTab', 'href', hit.newTabUrl);
// Show the Alignment box whenever a base-by-base alignment page is available (htcUserAli on a
// fresh search, htcBlatAlign on a shared-link reopen); hide it only if detailsUrl is missing.
var alignBox = document.getElementById('dvAlignBox');
if (alignBox) { alignBox.style.display = hit.detailsUrl ? '' : 'none'; }
if (hit.detailsUrl) {
blatSet('dvViewAlign', 'href', hit.detailsUrl);
blatSet('dvAlign', 'text',
'See the base-by-base alignment of your query against ' + hit.chrom +
': matches, mismatches and gaps across the whole span.');
}
}
function blatSelect(dt, rank) {
blatSelectedRank = rank;
$('#blatTable tbody tr').each(function() {
var d = dt.row(this).data();
$(this).toggleClass('blatSel', !!d && d.rank === rank);
});
var hit = hgBlatData.hits.find(h => h.rank === rank);
blatRenderDetail(hit);
}
// ---- header tooltips (reuse the browser's title -> mouseover system) -----
var BLAT_HEADER_TIPS = {
'#': 'Rank by the chosen sort order',
'Query': 'The query sequence this hit came from',
'Open in Genome Browser': 'Genomic location of the match (1-based). Click the position to ' +
'open the Genome Browser there, or the icon to open it in a new tab.',
'Show': 'Show the base-by-base alignment of your sequence to the genome',
'Locus': 'Nearest gene(s), and whether the hit falls in an exon, intron, or intergenic region',
'Score': 'BLAT score: matches minus mismatches and gap penalties. Higher is better.',
'Identity': 'Percent identity of the aligned bases',
'Strand': 'Genome strand the query matched (+ or -)',
'Query coverage': 'Which part of the query aligned (blue) across its full length',
'Span': 'Length of the match on the genome (bp). Larger than the query length means ' +
'the alignment crosses introns or deletions.'
};
function blatApplyTooltips() {
$('#blatTable thead th').each(function() {
var tip = BLAT_HEADER_TIPS[$(this).text().trim()];
if (tip) { $(this).attr('title', tip); }
});
if (typeof convertTitleTagsToMouseovers === 'function') {
convertTitleTagsToMouseovers();
}
}
// ---- share a link --------------------------------------------------------
function blatShareLink() {
// No session, no AJAX: the results page already has a stable, shareable URL (hgBlat.c emits it as
// cfg.shareUrl and blatBuild() pins it into the address bar with history.replaceState), so this
// just shows/copies window.location. The link reopens straight from the trash .pslx/.fa, so it
// works until those trash files are cleaned - hence the retention note.
- var box = document.getElementById('blatShareBox');
+ var box = document.getElementById('gbShareBox');
if (!box) { return; }
if (box.style.display === 'flex') { box.style.display = 'none'; return; } // toggle off
var url = window.location.href;
box.style.display = 'flex';
box.innerHTML =
- 'Shareable link — anyone with it can reopen ' +
+ 'Shareable link — anyone with it can reopen ' +
'these results. The results are stored temporarily, so the link works for at least 48 hours ' +
'after they were last viewed.' +
- '' +
- '';
- var inp = document.getElementById('blatShareInput');
+ '' +
+ '';
+ var inp = document.getElementById('gbShareInput');
inp.value = url;
inp.focus();
inp.select();
$('#blatShareCopy').on('click', function() {
inp.select();
if (navigator.clipboard) { navigator.clipboard.writeText(url); }
else { document.execCommand('copy'); }
this.textContent = 'Copied';
});
}
// ---- Rename BLAT track (modal) -------------------------------------------
// The results custom track is built (and renamed) by hgBlat.c's inline code, which exposes a small
// window.blatRenameCt(name, description) helper (it POSTs to hgc's buildBigPsl and rebuilds the
// track). We reuse that helper (no new endpoint), just swapping its old inline toggle-form UI for a
// proper modal dialog. The current name/description come from cfg (hgBlat.c), not a global, so this
// does not depend on any generic page-global.
function blatRenameModalHtml(cfg) {
// hgSession link is relative (same /cgi-bin/), carrying db + hgsid so the session page opens in
// this assembly and cart.
var sessionUrl = `hgSession?db=${encodeURIComponent(cfg.db)}&hgsid=${encodeURIComponent(cfg.hgsid)}`;
- return '
' +
- '
' +
- '
Rename BLAT Track
' +
- '
Every BLAT result is stored in its own track in the Genome ' +
+ return '
' +
+ '
' +
+ '
Rename BLAT Track
' +
+ '
Every BLAT result is stored in its own track in the Genome ' +
'Browser. You can rename the track here. Results will disappear after 2–3 days, unless ' +
`they are saved into a Session link.
` +
- '' +
- '' +
- '' +
- '' +
- '
' +
- '' +
- '' +
+ '' +
+ '' +
+ '' +
+ '' +
+ '
' +
+ '' +
+ '' +
'
';
}
function blatCloseRename() {
- var bg = document.getElementById('blatModalBg');
+ var bg = document.getElementById('gbModalBg');
if (bg) { bg.style.display = 'none'; }
}
function blatOpenRename() {
- var bg = document.getElementById('blatModalBg');
+ var bg = document.getElementById('gbModalBg');
if (!bg) { return; }
// Pre-fill with the track's current name/description (emitted by hgBlat.c in cfg).
var cfg = hgBlatData.config;
document.getElementById('blatRenameName').value = cfg.trackName || '';
document.getElementById('blatRenameDesc').value = cfg.trackDescription || '';
bg.style.display = 'flex';
document.getElementById('blatRenameName').focus();
document.getElementById('blatRenameName').select();
}
function blatWireRename() {
$('#blatRenameBtn').on('click', blatOpenRename);
$('#blatRenameCancel').on('click', blatCloseRename);
// Click on the dark backdrop (but not the dialog itself) closes.
- $('#blatModalBg').on('click', function(ev) {
+ $('#gbModalBg').on('click', function(ev) {
if (ev.target === this) { blatCloseRename(); }
});
$(document).on('keydown.blatRename', function(ev) {
- var bg = document.getElementById('blatModalBg');
+ var bg = document.getElementById('gbModalBg');
if (bg && bg.style.display !== 'none' && ev.key === 'Escape') { blatCloseRename(); }
});
$('#blatRenameOk').on('click', function() {
var name = document.getElementById('blatRenameName').value.trim();
var desc = document.getElementById('blatRenameDesc').value.trim();
if (!name) { document.getElementById('blatRenameName').focus(); return; }
// Reuse hgBlat.c's window.blatRenameCt(name, description): rebuilds the custom track under the
// new name via the existing hgc buildBigPsl call. Keep cfg in sync so a re-open of the modal
// shows the new values.
if (typeof window.blatRenameCt === 'function') {
hgBlatData.config.trackName = name;
hgBlatData.config.trackDescription = desc;
window.blatRenameCt(name, desc);
}
blatCloseRename();
});
}
// ---- FASTA viewer (generic) ----------------------------------------------
function blatToFasta(seqs) {
// seqs: [{name, seq}, ...] -> FASTA text, sequence wrapped at 60 chars per line.
return seqs.map(function(s) {
var body = String(s.seq || '').toUpperCase().replace(/(.{60})/g, '$1\n').replace(/\n$/, '');
return '>' + s.name + '\n' + body;
}).join('\n');
}
function blatShowFasta(box, seqs, fileName) {
// Render seqs as FASTA inside `box`, with Copy-to-clipboard and Download buttons. Generic — takes
// any [{name, seq}] list so it can be reused for other sequences later.
var fasta = blatToFasta(seqs);
box.style.display = 'flex';
box.innerHTML =
'
';
var ta = document.getElementById('blatSeqText');
ta.value = fasta;
document.getElementById('blatSeqCopy').addEventListener('click', function() {
ta.select();
if (navigator.clipboard) { navigator.clipboard.writeText(fasta); }
else { document.execCommand('copy'); }
this.textContent = 'Copied';
});
document.getElementById('blatSeqDownload').addEventListener('click', function() {
var a = document.createElement('a');
a.href = URL.createObjectURL(new Blob([fasta], { type: 'text/plain' }));
a.download = fileName || 'query.fa';
document.body.appendChild(a);
a.click();
document.body.removeChild(a);
setTimeout(function() { URL.revokeObjectURL(a.href); }, 0);
});
document.getElementById('blatSeqClose').addEventListener('click', function() {
box.style.display = 'none';
});
}
function blatShowQuerySeq() {
var box = document.getElementById('blatSeqBox');
if (box.style.display === 'flex') { box.style.display = 'none'; return; } // toggle off
blatShowFasta(box, hgBlatData.config.querySeqs, 'blatQuery.fa');
}
// ---- build ---------------------------------------------------------------
function blatBuild() {
var cfg = hgBlatData.config;
var hits = hgBlatData.hits;
// Pin a stable, shareable URL into the address bar (no server redirect) so refresh, bookmark and
// "Share a link" all use the trash-backed reopen link instead of the transient POST/search URL.
if (cfg.shareUrl) {
try { history.replaceState(null, '', cfg.shareUrl); } catch (e) { /* older browsers: ignore */ }
}
var back = cfg.backUrl ?
- `Back to Genome Browser` : '';
// The page actions live in the gold main-header bar (framework #sectTtl), next to the title -
// so there is no separate toolbar (.blatHead is gone). Injected into #sectTtl below.
var headActions =
- `${back}New BLAT search`;
+ `${back}New BLAT search`;
// Top banner: note this is the new page, link back to the classic page (fresh searches only,
// where the trash files still exist), and invite feedback. The old page also clears the
// blatNewPage preference so later searches use the classic page until the user opts back in.
var origPage = cfg.canOldPage ?
` You can go back to the original page anytime.` : '';
var bannerHtml =
- `
We are testing a new BLAT output page.${origPage} ` +
+ `
We are testing a new BLAT output page.${origPage} ` +
`If you have feedback on this new page, do not hesitate to let us know via ` +
`genome@soe.ucsc.edu.
`;
var queryCount = new Set(hits.map(h => h.qName)).size;
var th = [];
th.push('
#
');
if (cfg.multiQuery) { th.push('
Query
'); }
th.push('
Open in Genome Browser
');
th.push('
Show
');
th.push('
Query coverage
');
if (cfg.hasLocus) { th.push('
Locus
'); }
th.push('
Score
');
th.push('
Identity
');
th.push('
Strand
');
th.push('
Span
');
// detail dock sits above the table: with long hit lists a bottom dock scrolls out of view
document.getElementById('blatResults').innerHTML =
bannerHtml +
- `
` +
(cfg.canRename ? blatRenameModalHtml(cfg) : '');
// Put the page actions in the gold main-header bar, to the right of the title (framework #sectTtl).
var sectTtl = document.getElementById('sectTtl');
if (sectTtl) {
var acts = document.createElement('span');
acts.className = 'blatHeadActions';
acts.innerHTML = headActions;
sectTtl.appendChild(acts);
}
$('#blatShareBtn').on('click', blatShareLink);
$('#blatSeqBtn').on('click', blatShowQuerySeq);
blatWireRename();
var columns = [];
columns.push({ data: 'rank', className: 'num rankCol' });
if (cfg.multiQuery) { columns.push({ data: 'qName', className: 'queryCol' }); }
columns.push({ data: null, orderable: false, className: 'blatPos',
render: (d, type, row) => (type === 'display' ? blatPositionCell(row) : row.chrom + ':' + row.tStart) });
columns.push({ data: null, orderable: false, className: 'actionsCol',
render: (d, type, row) => (type === 'display' ? blatActionsCell(row) : '') });
columns.push({ data: null, className: 'covCol', orderable: false,
render: (d, type, row) => (type === 'display' ? blatCoverageCell(row) :
(row.qEnd - row.qStart + 1)) });
if (cfg.hasLocus) {
columns.push({ data: 'locusText',
render: (d, type, row) => (type === 'display' ? blatLocusCell(row) : (d || '')) });
}
// Score carries a bar scaled to the highest score in this result set (raw score kept for sorting).
var maxScore = hits.reduce((m, h) => Math.max(m, h.score || 0), 0);
columns.push({ data: 'score', className: 'num scoreCol',
render: (d, type, row) => (type === 'display' ? blatScoreCell(row, maxScore) : d) });
columns.push({ data: 'identity', className: 'num identCol',
render: (d, type, row) => (type === 'display' ? blatIdentityCell(row) : d) });
columns.push({ data: 'strand', className: 'strandCol' });
columns.push({ data: 'span', className: 'num',
render: (d, type, row) => (type === 'display' ? blatFmt(d) : d) });
var dt = $('#blatTable').DataTable({
data: hits,
columns: columns,
paging: false,
info: false,
order: [],
language: { search: '', searchPlaceholder: 'Filter hits by locus, chrom, position…' }
});
$('#blatTable tbody').on('click', 'tr', function(ev) {
if ($(ev.target).closest('a').length) { return; } // let links work normally
var d = dt.row(this).data();
if (d) { blatSelect(dt, d.rank); }
});
// Keep the selected-row highlight after sort/filter. Header tooltips are wired once below (the
// persists across draws); we deliberately do NOT re-run convertTitleTagsToMouseovers on
// every draw, as it re-scans the whole document and adds global listeners on each call.
dt.on('draw', function() {
if (blatSelectedRank !== null) { blatSelect(dt, blatSelectedRank); }
});
// No hit is pre-selected: several hits are often tied on score/identity, so picking one for the
// user is misleading. The detail panel shows a prompt until a row is clicked.
document.getElementById('blatDetail').innerHTML =
`
Click a hit below to see its alignment details. ` +
`If you are missing matches that you think should be there, ` +
`read our BLAT FAQ or ` +
`contact us.
`;
blatApplyTooltips();
}
// ==== search form (the input page) ========================================
// hgBlat.c emits var hgBlatFormData = {...} together with a real