4bd85aa14161039a40fd499bd8416ab51f099d81
braney
Sat Jul 25 18:34:48 2026 -0700
add Docent, a language for authoring Genome Browser tours refs #37892
A Docent script is an ordered list of high-level verbs (go, hide, track,
mouseover, convert, drag, shot) that drives a real browser against a real
server, and renders to a silent mp4 plus a named PNG still at every shot
marker. One source, both outputs, so a published figure is a frame of the
tour and the two cannot drift apart.
The verbs encode browser mechanics rather than selectors. convert: knows the
Hide-defaults checkbox reverts when the Assembly menu reloads, track: {clinvar:
pack} knows that composite's clean parameter set, and mouseover: knows a lifted
track's DOM id gains a per-run hub_<n>_ prefix. The author writes intent.
The surface syntax is YAML so ordinary editors highlight it; the language is
the verb vocabulary on top, not the serialization. Scripts are named
<base>.docent.yaml.
This was built inside the quickLift Current Protocols paper repo, where it
still has its six working scripts, and only the general parts move here: the
renderer, the language reference, and the make rules a project includes to get
incremental rebuilds. Nothing in the build refers to the directory, the same
way cartTrackVarCatalog does not, since these are node scripts and need
playwright and js-yaml.
target: defaults to genome-test rather than the sandbox it grew up on, and
resolves any hgwdev-<user> name, so a script that forgets to say where it runs
does not quietly hit somebody's machine.
Next step is #37838. Today a step reaches the browser as CGI variables, which
is why the verbs have to know each composite by heart; once the cart takes a
structured blob a step can name the state it wants instead.
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
diff --git src/hg/utils/docent/docent.js src/hg/utils/docent/docent.js
new file mode 100755
index 00000000000..e07bf093564
--- /dev/null
+++ src/hg/utils/docent/docent.js
@@ -0,0 +1,758 @@
+#!/usr/bin/env node
+/* docent.js SCRIPT.docent.yaml [OUT.mp4]
+ *
+ * Docent -- a language for authoring guided tours of the UCSC Genome Browser.
+ *
+ * Render a hand-authored Docent script into a silent mp4 PLUS a named still PNG at
+ * every `shot:` marker (the figures). One source script -> both outputs, so a figure
+ * is literally a frame of the tour. Reuses the shared Playwright/Chromium in ~/pwrec.
+ *
+ * PLAYWRIGHT_BROWSERS_PATH=~/pwrec/browsers NODE_PATH=~/pwrec/node_modules \
+ * node docent.js AP1.docent.yaml
+ *
+ * The high-level verbs bake in the quickLift/Convert mechanics (dbSNP composite
+ * params, the hideDefaults-reverts-on-assembly-change bug, target lookup) so the
+ * author writes intent, not selectors. See README.md for the language.
+ *
+ * The surface syntax is YAML so ordinary editors highlight it; the language is the
+ * verb vocabulary layered on top, not the serialization. Scripts are named
+ * <base>.docent.yaml (a bare <base>.docent also works).
+ */
+const { chromium } = require('playwright');
+const yaml = require('js-yaml');
+const fs = require('fs');
+const path = require('path');
+const { execFileSync } = require('child_process');
+
+// ---------- parse script + config ----------
+const SCRIPT = process.argv[2];
+if (!SCRIPT) { console.error('usage: node docent.js SCRIPT.docent.yaml [OUT.mp4]'); process.exit(2); }
+const doc = yaml.load(fs.readFileSync(SCRIPT, 'utf8')) || {};
+
+// Lint: in a YAML flow map a colon needs a trailing space, so `{item:name5568747}`
+// parses as ONE key "item:name5568747" (value null) and the intended `item:` arg is
+// silently dropped -- the verb then quietly falls back to a default. Catch that here
+// (before the long browser run) by flagging any arg key that contains a ':'.
+(function lintSteps(steps) {
+ let n = 0;
+ const scan = (obj, where) => {
+ if (!obj || typeof obj !== 'object') return;
+ for (const k of Object.keys(obj)) {
+ if (typeof k === 'string' && k.includes(':')) {
+ n++;
+ console.warn(`WARNING ${where}: key "${k}" contains ':' -- a YAML flow map needs a `
+ + `space after the colon. Did you mean "${k.replace(/:(?=\S)/, ': ')}"? `
+ + `(this key is being IGNORED, so the verb may fall back to a default)`);
+ }
+ scan(obj[k], where);
+ }
+ };
+ (steps || []).forEach((s, i) => {
+ if (s && typeof s === 'object') { const v = Object.keys(s)[0]; scan(s[v], `step ${i + 1} (${v})`); }
+ });
+ if (n) console.warn(`(${n} suspicious key${n > 1 ? 's' : ''} above -- fix the missing space, or the arg is dropped)`);
+})(doc.steps);
+const HERE = path.dirname(path.resolve(SCRIPT));
+const base = path.basename(SCRIPT).replace(/\.(docent\.)?ya?ml$/i, '').replace(/\.docent$/i, '');
+const FIGDIR = path.resolve(HERE, '..'); // figures dir beside the scripts
+const OUTMP4 = process.argv[3] || doc.mp4 || path.join(FIGDIR, base + '.mp4');
+const STILLDIR = doc.stills ? path.resolve(HERE, doc.stills) : path.join(HERE, 'stills', base);
+
+// `target:` takes a shorthand from this table, a bare `hgwdev-<user>` sandbox name
+// (expanded below), or a full https://.../cgi-bin URL. Default is genome-test, so a
+// script that forgets to say where it runs does not silently hit someone's sandbox.
+const SERVERS = {
+ 'rr': 'https://genome.ucsc.edu/cgi-bin',
+ 'genome-test': 'https://genome-test.gi.ucsc.edu/cgi-bin',
+ 'hgwdev': 'https://hgwdev.gi.ucsc.edu/cgi-bin',
+ 'hgwbeta': 'https://hgwbeta.soe.ucsc.edu/cgi-bin',
+};
+const resolveTarget = t => {
+ if (!t) return SERVERS['genome-test'];
+ if (SERVERS[t]) return SERVERS[t];
+ if (/^hgwdev-[a-z0-9._-]+$/i.test(t)) return `https://${t}.gi.ucsc.edu/cgi-bin`; // personal sandbox
+ return t; // full URL
+};
+const SERVER = resolveTarget(doc.target).replace(/\/$/, '');
+const [VW, VH] = doc.size || [1000, 760];
+const PIX = doc.pix || 850;
+const PACE = Math.round((doc.pace ?? 1.2) * 1000); // dwell after each step
+const SHOTHOLD = Math.round((doc.shotHold ?? 2.2) * 1000); // extra dwell (pause) at a shot
+
+// track-name -> cart params (composite tracks expand to their learned "clean" config)
+const TRACKS = {
+ mane: m => [`mane=${m}`],
+ dbSnp155: m => [`dbSnp155Composite=${m}`, `dbSnp155Common=${m}`, `dbSnp155ViewVariants=${m}`, `dbSnp155ViewErrs=hide`],
+ clinvar: m => [`clinvar=${m}`, `clinvarMain=dense`, `clinvarSubLolly=${m}`, `clinvarCnv=hide`],
+};
+// The control-dropdown name and the data-image id can differ from the shortcut name:
+// composites are turned on via their composite cart var, and dbSNP's visible pixels
+// live in the "Common" subtrack's data image.
+const CTRL = { dbSnp155: 'dbSnp155Composite' }; // select[name=...] in the track controls
+const DATAIMG = { dbSnp155: 'dbSnp155Common', clinvar: 'clinvarMain' }; // #img_data_... that holds the drawn items
+const ctrlName = t => CTRL[t] || t;
+const imgTrack = t => DATAIMG[t] || t;
+
+const sleep = ms => new Promise(r => setTimeout(r, ms));
+const enc = s => encodeURIComponent(String(s));
+const state = { db: doc.db || 'hg38', position: doc.position || '', hgsid: '' };
+
+// ---------- animated cursor (same technique as the walkthrough-video skill's record.js) ----------
+const CURSOR_INIT = () => {
+ const add = () => {
+ if (document.getElementById('__cur')) return;
+ const c = document.createElement('div');
+ c.id = '__cur';
+ c.style.cssText = 'position:fixed;left:0;top:0;z-index:2147483647;pointer-events:none;width:24px;height:24px;margin-left:-3px;margin-top:-2px;filter:drop-shadow(0 1px 1px rgba(0,0,0,.4));';
+ c.innerHTML = '<svg width="24" height="24" viewBox="0 0 24 24"><path d="M3 2 L3 19 L7.5 14.5 L10.5 21.5 L13.5 20.2 L10.6 13.5 L17 13.5 Z" fill="#111" stroke="#fff" stroke-width="1.3"/></svg>';
+ document.documentElement.appendChild(c);
+ const place = (x, y) => { c.style.transform = `translate(${x}px,${y}px)`; };
+ place(120, 120);
+ document.addEventListener('mousemove', e => place(e.clientX, e.clientY), true);
+ document.addEventListener('mousedown', e => {
+ const r = document.createElement('div');
+ r.style.cssText = `position:fixed;left:${e.clientX}px;top:${e.clientY}px;z-index:2147483645;pointer-events:none;width:6px;height:6px;margin:-3px 0 0 -3px;border:3px solid rgba(225,30,30,.95);border-radius:50%;`;
+ document.documentElement.appendChild(r);
+ r.animate([{ transform: 'scale(1)', opacity: 1 }, { transform: 'scale(6)', opacity: 0 }], { duration: 520, easing: 'ease-out' });
+ setTimeout(() => r.remove(), 540);
+ }, true);
+ };
+ if (document.readyState === 'loading') document.addEventListener('DOMContentLoaded', add);
+ else add();
+};
+
+function absurl(u) {
+ if (/^https?:/.test(u)) return u;
+ if (u.startsWith('/cgi-bin/')) return SERVER.replace(/\/cgi-bin$/, '') + u;
+ if (u.startsWith('/')) return SERVER.replace(/\/cgi-bin$/, '') + u;
+ return SERVER + '/' + u;
+}
+
+(async () => {
+ fs.mkdirSync(STILLDIR, { recursive: true });
+ const browser = await chromium.launch({ headless: true, args: ['--force-color-profile=srgb'] });
+ const ctx = await browser.newContext({
+ viewport: { width: VW, height: VH }, deviceScaleFactor: 1,
+ recordVideo: { dir: path.join(HERE, '.vid_' + base), size: { width: VW, height: VH } },
+ });
+ await ctx.addInitScript(CURSOR_INIT);
+ await ctx.addInitScript(() => { try { localStorage.setItem('hgTracks_hideTutorial', '1'); } catch (e) {} });
+ const page = await ctx.newPage();
+ const cur = { x: 120, y: 120 };
+ const pinnedTips = []; // recorded mouseover tooltips for the next pinShot (per view)
+
+ async function captureState() {
+ try {
+ const u = new URL(page.url());
+ const h = u.searchParams.get('hgsid'); if (h) state.hgsid = h;
+ const db = u.searchParams.get('db'); if (db) state.db = db;
+ const p = u.searchParams.get('position'); if (p) state.position = p;
+ } catch (e) {}
+ // An interactive zoom / drag-select reload stores the new window in the CART, not the
+ // URL, so read the live position straight from hgTracks when we're on a tracks page --
+ // otherwise a later position-based nav (e.g. turning on a track) reverts the zoom.
+ try {
+ const pos = await page.evaluate(() => {
+ try { if (typeof hgTracks !== 'undefined' && hgTracks.chromName)
+ return hgTracks.chromName + ':' + (hgTracks.winStart + 1) + '-' + hgTracks.winEnd; } catch (_) {}
+ return null;
+ });
+ if (pos) state.position = pos;
+ } catch (e) {}
+ }
+ async function nav(u) { pinnedTips.length = 0; await page.goto(absurl(u), { waitUntil: 'load' }); await captureState(); await page.mouse.move(cur.x, cur.y); }
+ async function glide(x, y) {
+ const steps = Math.max(10, Math.round(Math.hypot(x - cur.x, y - cur.y) / 9));
+ for (let i = 1; i <= steps; i++) { await page.mouse.move(cur.x + (x - cur.x) * i / steps, cur.y + (y - cur.y) * i / steps); await sleep(15); }
+ cur.x = x; cur.y = y;
+ }
+ async function glideTo(sel) {
+ const b = await page.locator(sel).first().boundingBox({ timeout: 8000 }).catch(() => null);
+ if (b) await glide(b.x + b.width / 2, b.y + b.height / 2);
+ }
+ async function clickGlide(sel) { await glideTo(sel); await sleep(160); await page.click(sel); }
+ async function checkGlide(sel, want) {
+ await glideTo(sel); await sleep(140);
+ if (want) await page.check(sel).catch(() => {}); else await page.uncheck(sel).catch(() => {});
+ }
+ // visibly open a native <select>, highlight the target, (optionally) commit, collapse.
+ // commit=false leaves the real value untouched (just shows the pick) -- used for the
+ // track-controls gesture, where the actual state is applied by a follow-up nav().
+ async function openSelectVisible(sel, val, rows = 12, commit = true) {
+ const loc = page.locator(sel).first();
+ await loc.evaluate(el => { try { el.scrollIntoView({ block: 'center' }); } catch (e) { el.scrollIntoView(); } });
+ await sleep(350); await glideTo(sel); await sleep(300);
+ await loc.evaluate((el, r) => {
+ const b = el.getBoundingClientRect();
+ el.dataset._sz = el.size || 1; el.dataset._cs = el.style.cssText;
+ el.style.position = 'fixed'; el.style.left = b.left + 'px'; el.style.top = b.top + 'px';
+ el.style.width = 'auto'; el.style.minWidth = b.width + 'px'; el.style.zIndex = '2147483646';
+ el.style.background = '#fff'; el.style.border = '1px solid #888'; el.style.boxShadow = '0 4px 12px rgba(0,0,0,.35)';
+ el.size = Math.min(r, el.options.length);
+ }, rows);
+ await sleep(650);
+ await loc.evaluate((el, v) => { const i = [...el.options].findIndex(o => o.value === v); if (i >= 0) { el.selectedIndex = i; try { el.options[i].scrollIntoView({ block: 'center' }); } catch (e) {} } }, val);
+ await sleep(1000);
+ if (commit) {
+ await loc.evaluate((el, v) => { el.value = v; el.dispatchEvent(new Event('change', { bubbles: true })); }, val);
+ await sleep(250);
+ }
+ await loc.evaluate(el => { el.size = parseInt(el.dataset._sz) || 1; el.style.cssText = el.dataset._cs || ''; }).catch(() => {});
+ }
+ async function shot(name) {
+ const p = path.join(STILLDIR, name + '.png');
+ // If a mouseover tooltip is currently up, capture the image + tooltip together
+ // (the tooltip is appended to <body>, so an #imgTbl element shot would clip it).
+ const clip = await page.evaluate(() => {
+ const im = document.getElementById('imgTbl');
+ if (!im) return null;
+ // Floating overlays to capture together with the image: the mouseover tooltip,
+ // and any visible jQuery-UI dialog (e.g. the drag-select "Zoom In / Highlight" box).
+ const overlays = [];
+ const tip = document.getElementById('mouseoverContainer');
+ if (tip && tip.offsetWidth > 0 &&
+ getComputedStyle(tip).display !== 'none' && getComputedStyle(tip).visibility !== 'hidden') overlays.push(tip);
+ for (const d of document.querySelectorAll('.ui-dialog')) if (d.offsetWidth > 0) overlays.push(d);
+ if (!overlays.length) return null;
+ const a = im.getBoundingClientRect();
+ let x = a.left, y = a.top, x2 = a.right, y2 = a.bottom;
+ for (const o of overlays) { const r = o.getBoundingClientRect(); x = Math.min(x, r.left); y = Math.min(y, r.top); x2 = Math.max(x2, r.right); y2 = Math.max(y2, r.bottom); }
+ return { x: Math.max(0, x - 4), y: Math.max(0, y - 4), width: (x2 - x) + 8, height: (y2 - y) + 8 };
+ });
+ if (clip) {
+ await page.screenshot({ path: p, clip });
+ } else {
+ const el = (await page.locator('#imgTbl').count()) ? page.locator('#imgTbl') : page.locator('main');
+ await el.screenshot({ path: p });
+ }
+ console.log('SHOT', p);
+ await sleep(SHOTHOLD);
+ }
+ // Resolve a track name to its DOM key + data-image and row bounding boxes. On a
+ // quickLift/Convert target the tracks come from a hub, so ids gain a dynamic
+ // `hub_<n>_` prefix -- match by suffix so the YAML can just say `track: quickLiftChain`.
+ async function trackBox(t) {
+ const want0 = imgTrack(t);
+ const key = await page.evaluate(k => {
+ if (document.getElementById('img_data_' + k)) return k;
+ const el = [...document.querySelectorAll('[id^="img_data_"]')]
+ .find(e => e.id === 'img_data_' + k || e.id.endsWith('_' + k));
+ return el ? el.id.replace('img_data_', '') : k;
+ }, want0);
+ const img = await page.locator(`#img_data_${key}`).first().boundingBox({ timeout: 8000 }).catch(() => null);
+ const row = await page.locator(`#imgTbl tr#tr_${key}`).first().boundingBox({ timeout: 8000 }).catch(() => null);
+ if (!img || !row) throw new Error(`track "${t}" not shown (need #img_data_${key} + #tr_${key})`);
+ return { key, img, row };
+ }
+ // Resolve a NAMED item to a point {x,y} + its map-box HREF (the item's hgc link). We
+ // pick the map <area> whose href(&i=<name>)/title carries the name AND whose box sits in
+ // this track's own ROW band (so stacked items on other rows don't win); fall back to the
+ // JSON mouseOver spans (wig/dense tracks, no per-item href).
+ async function itemXY(t, want, titleOnly) {
+ const { key, img, row } = await trackBox(t);
+ const band = { top: row.y, bot: row.y + row.height };
+ const area = await page.evaluate(({ want, titleOnly, band, imgBox }) => {
+ const areas = [...document.querySelectorAll('map[name^="map_"] area')];
+ const cands = [];
+ for (const a of areas) {
+ const href = a.getAttribute('href') || '';
+ const title = a.getAttribute('title') || a.getAttribute('data-tooltip') || '';
+ const hay = titleOnly ? title : (href + ' ' + title);
+ if (!hay.includes(want)) continue;
+ const c = (a.getAttribute('coords') || '').split(',').map(Number);
+ if (c.length < 4) continue;
+ // origin = the image this map is attached to (fall back to the data image box)
+ const m = a.closest('map'), nm = m && m.getAttribute('name');
+ const im = nm && document.querySelector(`img[usemap="#${nm}"]`);
+ const r = im ? im.getBoundingClientRect() : null;
+ const ox = r ? r.left : imgBox.x, oy = r ? r.top : imgBox.y;
+ const cx = ox + (c[0] + c[2]) / 2, cy = oy + (c[1] + c[3]) / 2;
+ cands.push({ cx, cy, href, inBand: cy >= band.top - 1 && cy <= band.bot + 1 });
+ }
+ const inBand = cands.filter(h => h.inBand);
+ return (inBand[0] || cands[0]) || null;
+ }, { want: String(want), titleOnly: !!titleOnly, band, imgBox: img });
+ if (area) return { x: area.cx, y: area.cy, href: area.href };
+ const span = await page.evaluate(({ keys, want }) => {
+ const md = window.mapData; if (!md || !md.spans) return null;
+ for (const k of keys) {
+ const arr = md.spans[k]; if (!arr) continue;
+ const s = arr.find(r => String(r.value || '').includes(want));
+ if (s) return { x1: s.x1, x2: s.x2 };
+ }
+ return null;
+ }, { keys: [key, t], want: String(want) });
+ if (!span) throw new Error(`item "${want}" not found in track "${t}" (searched map-box areas + mouseOver spans)`);
+ return { x: img.x + (span.x1 + span.x2) / 2, y: row.y + row.height / 2, href: null };
+ }
+ // POSITIONAL point: at:/frac:/x: -> x, y forced to the track row's middle. The grey
+ // side-label strip (insideX) is baked into the image's left, so a fraction/coord maps
+ // across [img.x+insideX, img.x+img.width], not the whole image width.
+ async function posXY(t, o) {
+ const { img, row } = await trackBox(t);
+ const insideX = await page.evaluate(() => { try { return hgTracks.insideX || 0; } catch (_) { return 0; } });
+ let x;
+ if (o.x != null) x = img.x + insideX + Number(o.x);
+ else {
+ const frac = (o.frac != null) ? Number(o.frac)
+ : (o.at != null) ? await page.evaluate(at => {
+ try { const s = hgTracks.winStart, e = hgTracks.winEnd;
+ const c = +String(at).replace(/.*:/, '').replace(/,/g, '');
+ return Math.max(0, Math.min(1, (c - s) / (e - s))); } catch (_) { return 0.5; }
+ }, o.at)
+ : 0.5;
+ x = img.x + insideX + frac * (img.width - insideX);
+ }
+ return { x, y: row.y + row.height / 2 };
+ }
+ // Hover an item to raise its mouseover tooltip (real mousemove -> the browser's own
+ // tooltip). Two ways to place the cursor:
+ // IDENTITY `item:` / `title:` / `value:` -> name the item (lands on the right ROW).
+ // POSITION `at:` (genomic coord) / `frac:` (0..1) / `x:` (raw px) -> a point.
+ async function mouseover(o) {
+ if (typeof o === 'string') o = { track: o };
+ o = o || {};
+ const t = o.track; if (!t) throw new Error('mouseover: needs a track');
+ const want = o.item ?? o.title ?? o.value; // identity mode if any is set
+ const { x, y } = (want != null)
+ ? await itemXY(t, want, o.title != null && o.item == null && o.value == null)
+ : await posXY(t, o);
+ // Dismiss any tooltip a previous mouseover left open (over the grey side-label strip,
+ // which has no items) so THIS item raises a FRESH tooltip -- otherwise a back-to-back
+ // pinned mouseover can capture the previous item's stale popup text.
+ await page.mouse.move(2, y); cur.x = 2; cur.y = y; await sleep(120);
+ await glide(x, y);
+ // small jiggle so the mousemove handler definitely fires and positions the tooltip
+ await page.mouse.move(x + 1, y); await sleep(60); await page.mouse.move(x, y);
+ await page.waitForSelector('#mouseoverContainer', { state: 'visible', timeout: 2500 }).catch(() => {});
+ // Optionally RECORD this tooltip so a later `pinShot:` can show several mouseovers
+ // open together in one figure. We only record (position + the tooltip's own HTML)
+ // here -- nothing is injected into the recorded page, so the mp4 still shows just the
+ // transient native tooltip. `pin:` on the step overrides the document-level
+ // `pinMouseovers:` default. Records accumulate within a view and are cleared on nav.
+ const pin = (o.pin != null) ? o.pin : (doc.pinMouseovers === true);
+ if (pin) await recordTip(x, y);
+ await sleep(o.hold != null ? Number(o.hold) * 1000 : SHOTHOLD);
+ if (o.shot) await shot(o.shot);
+ }
+ // Grab the live mouseover tooltip's HTML and anchor it at the ITEM's coordinate (x,y
+ // that mouseover just hovered), expressed RELATIVE TO the track image (#imgTbl). The
+ // browser parks its own tooltip at a near-fixed spot, so two tips would stack; anchoring
+ // to the item keeps each pinned tooltip on its own feature (and robust to the throwaway
+ // page's image sitting at a different offset).
+ async function recordTip(x, y) {
+ const t = await page.evaluate(({ x, y }) => {
+ const c = document.getElementById('mouseoverContainer');
+ if (!c || !c.offsetWidth) return null;
+ const im = document.getElementById('imgTbl');
+ const ir = im ? im.getBoundingClientRect() : { left: 0, top: 0 };
+ return { dx: x - ir.left + 8, dy: y - ir.top + 8, html: c.outerHTML };
+ }, { x, y });
+ if (t) pinnedTips.push(t);
+ }
+ // Render every recorded tooltip open at once in a still, WITHOUT touching the recorded
+ // page (so the mp4 is unaffected): reload the current view on a throwaway page that
+ // shares the session cookie (cart), inject the recorded tooltips, screenshot, discard.
+ async function pinShot(name) {
+ if (!pinnedTips.length) { console.warn(`pinShot ${name}: no pinned mouseovers recorded (set pin: true / pinMouseovers: true)`); return; }
+ const url = page.url();
+ const ctx2 = await browser.newContext({ viewport: { width: VW, height: VH }, deviceScaleFactor: 1 });
+ await ctx2.addCookies(await ctx.cookies());
+ const pg2 = await ctx2.newPage();
+ await pg2.goto(url, { waitUntil: 'load' });
+ await pg2.waitForSelector('#imgTbl', { timeout: 8000 }).catch(() => {});
+ await pg2.evaluate((tips) => {
+ window.scrollTo(0, 0);
+ const im = document.getElementById('imgTbl');
+ const ir = im ? im.getBoundingClientRect() : { left: 0, top: 0 };
+ for (const t of tips) {
+ const wrap = document.createElement('div');
+ wrap.innerHTML = t.html;
+ const el = wrap.firstElementChild; if (!el) continue;
+ el.removeAttribute('id');
+ el.classList.add('__pinnedTip');
+ el.style.position = 'fixed';
+ el.style.left = (ir.left + t.dx) + 'px'; el.style.top = (ir.top + t.dy) + 'px';
+ el.style.opacity = '1'; el.style.visibility = 'visible';
+ el.style.display = 'inline-block'; el.style.pointerEvents = 'none';
+ document.documentElement.appendChild(el);
+ }
+ }, pinnedTips);
+ const p = path.join(STILLDIR, name + '.png');
+ const clip = await pg2.evaluate(() => {
+ const im = document.getElementById('imgTbl'); if (!im) return null;
+ const els = [im, ...document.querySelectorAll('.__pinnedTip')];
+ let x = Infinity, y = Infinity, x2 = -Infinity, y2 = -Infinity;
+ for (const o of els) { const r = o.getBoundingClientRect(); x = Math.min(x, r.left); y = Math.min(y, r.top); x2 = Math.max(x2, r.right); y2 = Math.max(y2, r.bottom); }
+ return { x: Math.max(0, x - 4), y: Math.max(0, y - 4), width: (x2 - x) + 8, height: (y2 - y) + 8 };
+ });
+ if (clip) await pg2.screenshot({ path: p, clip });
+ else await pg2.locator('#imgTbl').screenshot({ path: p });
+ await ctx2.close();
+ console.log('SHOT', p, `(pinned: ${pinnedTips.length})`);
+ pinnedTips.length = 0; // consume the set
+ }
+ // Shift+drag across the track image to open the browser's own drag-select dialog
+ // ("Zoom In / Single Highlight / ..."), then act on it. Endpoints are given as
+ // genomic coords (from:/to:), a fraction across the view (fromFrac:/toFrac:) or a
+ // raw pixel (fromX:/toX:). Optional `track:` picks the row the drag runs over (y);
+ // default is the middle of the image. `shot:` captures the open dialog (e.g. the
+ // Figure 1A drag-select box). `then:` = zoom (default, clicks Zoom In) | highlight
+ // (Single Highlight) | cancel (Escape, leaves the view unchanged).
+ async function drag(o) {
+ o = o || {};
+ const img = await page.locator('img[id^="img_data_"]').first().boundingBox({ timeout: 8000 }).catch(() => null);
+ const tbl = await page.locator('#imgTbl').first().boundingBox({ timeout: 8000 }).catch(() => null);
+ if (!img || !tbl) throw new Error('drag: track image not shown (need #imgTbl)');
+ const coordFrac = at => page.evaluate(a => {
+ try { const s = hgTracks.winStart, e = hgTracks.winEnd;
+ const c = +String(a).replace(/.*:/, '').replace(/,/g, '');
+ return Math.max(0, Math.min(1, (c - s) / (e - s))); } catch (_) { return null; }
+ }, at);
+ // The grey side-label strip is baked into the LEFT of every full-width track
+ // image, so the genomic data area starts insideX px in — fractions/coords map
+ // across [img.x+insideX, img.x+img.width], not the whole image width.
+ const insideX = await page.evaluate(() => { try { return hgTracks.insideX || 0; } catch (_) { return 0; } });
+ const dataLeft = img.x + insideX, dataW = Math.max(1, img.width - insideX);
+ const endX = async (px, fr, coord) => {
+ if (px != null) return img.x + Number(px);
+ const f = (fr != null) ? Number(fr) : (coord != null ? await coordFrac(coord) : null);
+ if (f == null) throw new Error('drag: need endpoints as coord (from:/to:), frac (fromFrac:/toFrac:) or px (fromX:/toX:)');
+ return dataLeft + f * dataW;
+ };
+ const x1 = await endX(o.fromX, o.fromFrac, o.from);
+ const x2 = await endX(o.toX, o.toFrac, o.to);
+ // y band for the drawn selection box. Default: span the FULL track image (like a
+ // real shift+drag, which highlights every track top-to-bottom). A named `track:`
+ // narrows the band to that one row instead. The CURSOR, however, sweeps near the
+ // TOP of the image (over the ruler) — a real drag is horizontal and the highlight
+ // fills downward on its own; sending the cursor to the vertical center would make
+ // it dive through the tracks first.
+ let y = tbl.y + Math.min(90, tbl.height / 2);
+ let y1 = 0, y2 = tbl.height;
+ if (o.track) {
+ const key = imgTrack(o.track);
+ const row = await page.locator(`#imgTbl tr#tr_${key}`).first().boundingBox().catch(() => null);
+ if (row) { y = row.y + row.height / 2; y1 = row.y - tbl.y; y2 = row.y - tbl.y + row.height; }
+ }
+ // The selected genomic range: from coord endpoints we already have it; otherwise
+ // derive it from the view fractions below (inside the browser).
+ const coordNum = v => +String(v).replace(/.*:/, '').replace(/,/g, '');
+ let posStr = null;
+ if (typeof o.from === 'string' && o.from.includes(':') && o.to != null) {
+ const chrom = o.from.split(':')[0], a = coordNum(o.from), b = coordNum(o.to);
+ posStr = `${chrom}:${Math.min(a, b)}-${Math.max(a, b)}`;
+ }
+ // Visible cursor sweep across the selection (no button-down — a real drag would
+ // just PAN the image). The drag-select band is grown UNDER the cursor as it moves,
+ // so it reads like a genuine shift+drag rather than popping in at the end; the
+ // dialog is then raised via the browser's own dragSelect entry point, the same way
+ // highlight_shot.js does it.
+ await glide(x1, y); await sleep(200);
+ // Arm the highlighting dialog and open a zero-width selection at the start point.
+ await page.evaluate(({ ix1, y1, y2 }) => {
+ try {
+ hgTracks.enableHighlightingDialog = true;
+ dragSelect.startTime = Date.now();
+ $(imageV2.imgTbl).imgAreaSelect({ x1: ix1, y1, x2: ix1, y2, show: true });
+ } catch (_) {}
+ }, { ix1: x1 - tbl.x, y1, y2 });
+ // Sweep to the end, widening the band to the cursor's x at every step.
+ const dsteps = Math.max(10, Math.round(Math.abs(x2 - x1) / 9));
+ for (let i = 1; i <= dsteps; i++) {
+ const px = x1 + (x2 - x1) * i / dsteps;
+ await page.mouse.move(px, y);
+ await page.evaluate(({ ix1, ix2, y1, y2 }) => {
+ try { $(imageV2.imgTbl).imgAreaSelect({ x1: Math.min(ix1, ix2), y1, x2: Math.max(ix1, ix2), y2, show: true }); } catch (_) {}
+ }, { ix1: x1 - tbl.x, ix2: px - tbl.x, y1, y2 });
+ await sleep(15);
+ }
+ cur.x = x2; cur.y = y;
+ await sleep(200);
+ // Band is fully drawn — now raise the Drag-and-select dialog.
+ const res = await page.evaluate(({ f1, f2, posStr }) => {
+ try {
+ let pos = posStr;
+ if (!pos) { const s = hgTracks.winStart, e = hgTracks.winEnd;
+ const c1 = Math.round(s + (e - s) * f1), c2 = Math.round(s + (e - s) * f2);
+ pos = hgTracks.chromName + ':' + (Math.min(c1, c2) + 1) + '-' + Math.max(c1, c2); }
+ dragSelect.selectionEndDialog(pos);
+ return true;
+ } catch (e) { return String((e && e.message) || e); }
+ }, { f1: (x1 - dataLeft) / dataW, f2: (x2 - dataLeft) / dataW, posStr });
+ const up = await page.waitForSelector('#dragSelectDialog:visible', { timeout: 4000 }).then(() => true).catch(() => false);
+ if (!up) throw new Error('drag: drag-select dialog did not open' + (res === true ? '' : ' (' + res + ')'));
+ await sleep(400);
+ if (o.shot) await shot(o.shot);
+ const act = o.then || 'zoom';
+ if (act === 'cancel') { await page.keyboard.press('Escape'); }
+ else {
+ const label = (act === 'highlight') ? 'Single Highlight' : 'Zoom In';
+ const sel = `.ui-dialog-buttonset button:has-text("${label}")`;
+ // "Zoom In" either full-submits the form OR does an AJAX in-place update
+ // (imageV2.inPlaceUpdate) that never fires a page load -- so don't wait on load;
+ // wait for the live hgTracks window to actually change from its pre-click value.
+ const before = await page.evaluate(() => { try { return hgTracks.winStart + '-' + hgTracks.winEnd; } catch (e) { return ''; } });
+ await clickGlide(sel);
+ if (act !== 'highlight') {
+ await page.waitForFunction(prev => {
+ try { return (hgTracks.winStart + '-' + hgTracks.winEnd) !== prev; } catch (e) { return false; }
+ }, before, { timeout: 8000 }).catch(() => {});
+ await page.waitForSelector('#imgTbl'); await sleep(400);
+ }
+ await captureState();
+ }
+ }
+ async function resolveTarget(to) {
+ if (/^GC[AF]_/i.test(to)) return to;
+ const matches = await page.$$eval('#hglft_toDbSelect option', (os, q) => {
+ const norm = t => t.toLowerCase().replace(/[^a-z0-9]+/g, ' ');
+ const toks = norm(q).trim().split(' ').filter(Boolean);
+ return os.filter(o => toks.every(tk => norm(o.text).includes(tk))).map(o => ({ v: o.value, t: o.text }));
+ }, String(to));
+ if (!matches.length) throw new Error('convert target not found in Assembly dropdown: ' + to);
+ if (matches.length > 1) {
+ console.warn(`WARNING: "${to}" matches ${matches.length} assemblies; using the first. Use an exact accession to disambiguate:`);
+ matches.forEach(m => console.warn(` ${m.v} ${m.t}`));
+ }
+ return matches[0].v;
+ }
+ async function convert(o) {
+ o = o || {};
+ try {
+ await glideTo('#view'); await page.hover('#view'); await sleep(900);
+ await clickGlide('a#convertMenuLink'); await page.waitForSelector('#hglft_toDbSelect', { timeout: 8000 });
+ } catch (e) {
+ await nav(`/cgi-bin/hgConvert?hgsid=${state.hgsid}&db=${state.db}&position=${enc(state.position)}`);
+ await page.waitForSelector('#hglft_toDbSelect');
+ }
+ const val = await resolveTarget(o.to);
+ await openSelectVisible('#hglft_toDbSelect', val);
+ await page.waitForSelector('#doQuickLift', { timeout: 8000 }).catch(() => {});
+ await sleep(400);
+ if (o.quicklift !== false) await checkGlide('#doQuickLift', true);
+ await checkGlide('#hideTracksOnConvert', o.hideDefaults !== false); // reverts on assembly change -> set explicitly
+ await sleep(300);
+ await clickGlide('#hglft_doConvert');
+ await page.waitForLoadState('load'); await captureState();
+ }
+
+ // On the "Hub Connect Successful" page, click the "Open:" link for `db` so the demo
+ // ends on the browser with the hub loaded. The links look like
+ // hgTracks?hubUrl=...&db=<genome>&position=lastDbPos (or &genome=<genome>).
+ async function openHubAssembly(db) {
+ const sel = await page.evaluate((db) => {
+ const esc = db.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+ const re = new RegExp('[?&](?:db|genome)=' + esc + '(?:&|$)');
+ // The connect page renders the genome list twice (a short + a collapsed long copy),
+ // so require the link to be VISIBLE, not just the first match in DOM order.
+ const a = [...document.querySelectorAll('a[href*="hgTracks"]')]
+ .find(a => re.test(a.getAttribute('href') || '') && a.getClientRects().length > 0);
+ if (!a) return null;
+ if (!a.id) a.id = '__hubOpen';
+ return '#' + a.id;
+ }, String(db));
+ if (!sel) return false;
+ await clickGlide(sel);
+ await page.waitForSelector('#imgTbl').catch(() => {});
+ await captureState();
+ return true;
+ }
+
+ function norm(step) {
+ if (typeof step === 'string') { const [v, ...r] = step.trim().split(/\s+/); return { verb: v, arg: r.length ? r.join(' ') : true }; }
+ const k = Object.keys(step)[0]; return { verb: k, arg: step[k] };
+ }
+ async function run({ verb, arg }) {
+ switch (verb) {
+ case 'gateway': await nav(`/cgi-bin/hgGateway?db=${state.db}`); break;
+ case 'go':
+ if (arg === true || arg === '' || arg == null) { await clickGlide('.jwGoButtonContainer'); await page.waitForSelector('#imgTbl'); }
+ else { await nav(`/cgi-bin/hgTracks?db=${state.db}&position=${enc(arg)}&pix=${PIX}`); }
+ await captureState(); break;
+ case 'hide': if (arg === 'all' || arg === true) { await clickGlide('#hgt\\.hideAll'); await page.waitForSelector('#imgTbl'); } break;
+ case 'track': {
+ const parts = [];
+ for (const [name, mode] of Object.entries(arg)) {
+ // Visible gesture: drive the real track-controls dropdown so the mouse is
+ // seen turning the track on. State is still applied by the nav() below
+ // (so composite "clean" configs come through), so this open is non-committing.
+ if (doc.trackAnim !== false) {
+ const csel = `select[name="${ctrlName(name)}"]`;
+ if (await page.locator(csel).count()) await openSelectVisible(csel, mode, 6, false);
+ }
+ const fn = TRACKS[name]; parts.push(...(fn ? fn(mode) : [`${name}=${mode}`]));
+ }
+ await nav(`/cgi-bin/hgTracks?db=${state.db}&position=${enc(state.position)}&${parts.join('&')}&pix=${PIX}`);
+ break;
+ }
+ case 'convert': await convert(arg); break;
+ case 'hub': {
+ // Attach a track hub by URL: hgTracks?hubUrl=... connects the hub and makes its
+ // tracks available at their hub-declared visibility. Follow with `track:` to turn
+ // specific ones on. Accepts a bare URL or {url:, db:, position:}.
+ const o = (typeof arg === 'string') ? { url: arg } : (arg || {});
+ if (!o.url) { console.warn('hub: no url given'); break; }
+ const db = o.db || state.db;
+ const pos = o.position != null ? o.position : state.position;
+ const parts = [`db=${db}`, `hubUrl=${enc(o.url)}`];
+ if (pos) parts.push(`position=${enc(pos)}`);
+ parts.push(`pix=${PIX}`);
+ await nav(`/cgi-bin/hgTracks?${parts.join('&')}`);
+ await page.waitForSelector('#imgTbl').catch(() => {});
+ break;
+ }
+ case 'addHub': {
+ // DEMONSTRATE attaching a hub through the UI (vs. `hub:` which just navs):
+ // My Data -> Track Hubs (hgHubConnect), the Connected Hubs tab, paste the URL,
+ // click Add Hub. The cursor glides and the URL is typed visibly. Accepts a bare
+ // URL or {url:, db:, shot:}.
+ const o = (typeof arg === 'string') ? { url: arg } : (arg || {});
+ if (!o.url) { console.warn('addHub: no url given'); break; }
+ const db = o.db || state.db;
+ await nav(`/cgi-bin/hgHubConnect?db=${db}`);
+ await clickGlide('a[href="#unlistedHubs"]'); // Connected Hubs tab reveals the URL box
+ await page.waitForSelector('#hubUrl', { state: 'visible', timeout: 8000 });
+ await glideTo('#hubUrl'); await page.click('#hubUrl'); await sleep(160);
+ await page.type('#hubUrl', String(o.url), { delay: 35 }); // visible typing
+ await sleep(300);
+ await clickGlide('#hubAddButton');
+ await page.waitForLoadState('load'); await captureState();
+ // Click through to the requested assembly so we end on the browser.
+ if (!await openHubAssembly(db))
+ console.warn(`addHub: no assembly link for db "${db}" on the connect page`);
+ if (o.shot) { await shot(o.shot); return; }
+ break;
+ }
+ case 'addPublicHub': {
+ // DEMONSTRATE connecting a PUBLIC hub via the UI: My Data -> Track Hubs, the
+ // Public Hubs tab, type search terms, click Search Public Hubs, then click Connect
+ // on the matching hub row. Bare string = search term (also used to match the row);
+ // map form {search:, match:, db:, shot:} lets you match a specific hub by label
+ // (the search often returns several hubs, so set `match:` to the hub's name).
+ const o = (typeof arg === 'string') ? { search: arg } : (arg || {});
+ const term = o.search != null ? o.search : null;
+ const match = o.match != null ? o.match : term;
+ if (!match) { console.warn('addPublicHub: no search/match given'); break; }
+ const db = o.db || state.db;
+ await nav(`/cgi-bin/hgHubConnect?db=${db}`);
+ await clickGlide('a[href="#publicHubs"]'); // Public Hubs tab (default, but show it)
+ await page.waitForSelector('#hubSearchTerms', { state: 'visible', timeout: 8000 });
+ if (term) {
+ await glideTo('#hubSearchTerms'); await page.click('#hubSearchTerms'); await sleep(120);
+ await page.type('#hubSearchTerms', String(term), { delay: 35 });
+ await sleep(250);
+ await clickGlide('#hubSearchButton');
+ await page.waitForLoadState('load');
+ }
+ // Click Connect on the row whose text contains `match` (don't guess a wrong hub).
+ const btnId = await page.evaluate((m) => {
+ m = String(m).toLowerCase();
+ for (const btn of document.querySelectorAll('input[name="hubConnectButton"]')) {
+ const tr = btn.closest('tr');
+ if (tr && tr.innerText.toLowerCase().includes(m)) return btn.id;
+ }
+ return null;
+ }, match);
+ if (!btnId) { console.warn(`addPublicHub: no public-hub row matching "${match}"`); break; }
+ await clickGlide('#' + btnId);
+ await page.waitForLoadState('load'); await captureState();
+ // Click through to the requested assembly so we end on the browser.
+ if (!await openHubAssembly(db))
+ console.warn(`addPublicHub: no assembly link for db "${db}" on the connect page`);
+ if (o.shot) { await shot(o.shot); return; }
+ break;
+ }
+ case 'addCustomTrack': {
+ // DEMONSTRATE loading a custom track via the UI: My Data -> Custom Tracks
+ // (hgCustom), paste the track data (or a data URL) into the box, click Submit,
+ // then click through to the browser. Accepts a bare string (the track text or a
+ // URL) or {data:/url:, db:, goto: first|current, shot:}. `goto:` picks the landing
+ // button -- "Go to first annotation" (default) or "Return to current position".
+ const o = (typeof arg === 'string') ? { data: arg } : (arg || {});
+ const data = o.data != null ? o.data : o.url;
+ if (!data) { console.warn('addCustomTrack: no data/url given'); break; }
+ const db = o.db || state.db;
+ await nav(`/cgi-bin/hgCustom?db=${db}`);
+ const ta = 'textarea[name="hgct_customText"]';
+ await page.waitForSelector(ta, { state: 'visible', timeout: 8000 });
+ await glideTo(ta); await page.click(ta); await sleep(160);
+ // insertText inserts literally (tabs/newlines and all) -- page.type would fire a
+ // Tab key and move focus out of the textarea. Animate short pastes char-by-char.
+ const s = String(data);
+ if (s.length <= 400) { for (const ch of s) { await page.keyboard.insertText(ch); await sleep(12); } }
+ else { await page.keyboard.insertText(s); }
+ await sleep(300);
+ await clickGlide('#Submit');
+ await page.waitForLoadState('load');
+ // The manage page appears on success; click through to the browser (a data error
+ // re-shows the add page instead, so guard on the button being present).
+ const goSel = (o.goto === 'current') ? '#submitGoBack' : '#submit';
+ if (await page.locator(goSel).count()) {
+ await clickGlide(goSel);
+ await page.waitForSelector('#imgTbl').catch(() => {});
+ await captureState();
+ } else {
+ console.warn('addCustomTrack: submit did not reach the manage page (data error?)');
+ }
+ if (o.shot) { await shot(o.shot); return; }
+ break;
+ }
+ case 'drag': await drag(arg); break;
+ case 'open': if (arg === 'lift') { await clickGlide('main a[href*="hgTracks"]'); await page.waitForSelector('#imgTbl'); await captureState(); } break;
+ case 'zoom': { const btn = (arg === 'in') ? '#hgt\\.in2' : '#hgt\\.out2'; await clickGlide(btn); await page.waitForSelector('#imgTbl'); break; }
+ case 'shot': await shot(arg); return; // shot supplies its own dwell
+ case 'pinShot': await pinShot(arg); break; // combined figure, off the mp4 timeline
+ case 'mouseover': await mouseover(arg); return; // supplies its own dwell (o.hold)
+ // escape hatches
+ case 'goto': await nav(arg); break;
+ case 'click':
+ if (arg && typeof arg === 'object' && arg.track) {
+ // Click a NAMED track item -> follow its map-box link (e.g. the hgc detail page).
+ const it = await itemXY(arg.track, arg.item ?? arg.title ?? arg.value,
+ arg.title != null && arg.item == null && arg.value == null);
+ await glide(it.x, it.y); await sleep(200);
+ // A raw click on the data area is swallowed by hgTracks' drag-select handler, so
+ // follow the item's own map-box link (the hgc detail page) directly.
+ if (it.href) await nav(it.href);
+ else { await page.mouse.click(it.x, it.y); await page.waitForLoadState('load').catch(() => {}); await captureState(); }
+ if (arg.shot) { await shot(arg.shot); return; }
+ } else {
+ // Plain selector click. Strip target=_blank first so an external link (e.g. a
+ // dbSNP id -> NIH) navigates in THIS tab instead of a popup we can't screenshot,
+ // then wait out the navigation so a following shot captures the destination page
+ // (a no-op if the click didn't navigate).
+ await page.evaluate(s => document.querySelectorAll(s).forEach(e => e.removeAttribute('target')), arg).catch(() => {});
+ await clickGlide(arg);
+ await page.waitForLoadState('load').catch(() => {});
+ await captureState();
+ }
+ break;
+ case 'hover': await glideTo(arg); await page.hover(arg); break;
+ case 'wait': await page.waitForSelector(arg, { timeout: 15000 }); break;
+ case 'sleep': await sleep(Number(arg)); return;
+ default: console.warn('unknown verb:', verb);
+ }
+ await sleep(PACE);
+ }
+
+ if (doc.reset) await page.goto(absurl('/cgi-bin/cartReset?skipLs=1'), { waitUntil: 'domcontentloaded' });
+ const steps = doc.steps || [];
+ for (let i = 0; i < steps.length; i++) {
+ const s = norm(steps[i]);
+ try { await run(s); }
+ catch (e) { console.error(`step ${i + 1} (${s.verb}) failed:`, e.message); await ctx.close(); await browser.close(); process.exit(1); }
+ }
+
+ await page.waitForTimeout(300);
+ await ctx.close();
+ await browser.close();
+
+ // transcode webm -> silent mp4
+ const vdir = path.join(HERE, '.vid_' + base);
+ const webm = fs.readdirSync(vdir).filter(f => f.endsWith('.webm')).map(f => path.join(vdir, f)).sort((a, b) => fs.statSync(b).mtimeMs - fs.statSync(a).mtimeMs)[0];
+ const FF = execFileSync('python3', ['-c', 'import imageio_ffmpeg,sys;sys.stdout.write(imageio_ffmpeg.get_ffmpeg_exe())']).toString().trim();
+ execFileSync(FF, ['-y', '-loglevel', 'error', '-i', webm, '-c:v', 'libx264', '-pix_fmt', 'yuv420p', '-crf', '22', '-preset', 'veryfast', '-movflags', '+faststart', OUTMP4]);
+ fs.rmSync(vdir, { recursive: true, force: true });
+ console.log('DONE ->', OUTMP4, '| stills in', STILLDIR);
+})().catch(e => { console.error(e); process.exit(1); });