74dc80fd3bd2a70371fa75218347ddc45a556dde braney Wed Aug 5 07:28:59 2026 -0700 Docent: render a tour at print resolution, and make zoom wait for its redraw refs #37892 scale: k (DOCENT_SCALE=k, make hires [SCALE=3]) renders the same tour with k times the pixels, for figures that have to print -- a screen still is about 120 dpi across a journal column. Nothing is upscaled; each layer that draws is asked for more: * deviceScaleFactor: k with the viewport left at its 1x CSS size, so the page lays out exactly as at 1x -- same line breaks, same jQuery-dialog width, same tooltip placement -- and rasterizes with k times the pixels, * pix x k so the server draws a wider browser image, with textSize stepped up its ladder to match (3x lands on 24) so hgTracks makes the same layout decisions in it: same tick spacing, same room for labels, same packing of features into rows, * zoom: 1/k on the image table, handing that wider image the 1x amount of layout space, so one image pixel falls on one device pixel. A scaled run is stills-only (no mp4), and DOCENT_STILLS names a different parent so a print render lands beside the screen stills instead of over them. Everything hgTracks reports about the image -- map-box coords, mouseOver spans, insideX, a px: drag endpoint -- is in the pixels the SERVER drew, which is not the displayed size once the image is scaled. Those now go through the image's natural-to-displayed ratio (1 at 1x). Without it a named mouseover: lands k times off and pins a different feature. zoom: in|out waited only for #imgTbl, which the buttons never remove (they redraw in place via ajax), so the following step could read the previous window's map boxes and report an item "not found" that was simply not in view yet. It now waits for the window itself to change. Pre-existing, hidden by the dwell that FAST removes -- and every hires run is FAST. An item-not-found error also names the current window and the items that ARE in that row, which is what told the two cases apart. 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 index f4402c92bc3..9150f8fb1ff 100755 --- src/hg/utils/docent/docent.js +++ src/hg/utils/docent/docent.js @@ -1,1330 +1,1454 @@ #!/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 os = require('os'); 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); +// Stills go to stills/<base>/. DOCENT_STILLS names a different PARENT ("stills.hires"), +// which is how a high-resolution run keeps its figures beside the screen-resolution ones +// instead of overwriting them. +const STILLPARENT = process.env.DOCENT_STILLS; +const STILLDIR = STILLPARENT ? path.resolve(HERE, STILLPARENT, base) + : 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(/\/$/, ''); +// SCALE: the same tour rendered at k times the resolution, for figures that have to print. +// Nothing is upscaled -- a still only ever has the pixels it was drawn with -- so each layer +// is asked to draw k times as many while the layout is left alone: +// +// * deviceScaleFactor: k. The viewport keeps its 1x CSS size, so the page lays out exactly +// as at 1x -- same line breaks, same jQuery-dialog width, same tooltip placement -- and +// every bit of it is rasterized with k times the pixels. The retina case, natively. +// * `pix` x k, so the server draws the browser image k times as wide, with `textSize` +// stepped up to match so hgTracks makes the SAME layout decisions in that bigger image: +// same tick spacing, same room for labels, same packing of features into rows. Without +// the font, a wider image is a different picture rather than a bigger one. +// * `zoom: 1/k` on the image table (SCALE_INIT below), handing that k-times-wider image +// back the 1x amount of layout space. One image pixel then falls on exactly one device +// pixel: native resolution, no resampling anywhere in the path. +// +// So the still comes out k times the 1x still in each dimension, showing the same figure -- +// not a variation of it rendered in a bigger window. +const SCALE = Math.max(1, Number(process.env.DOCENT_SCALE || doc.scale || 1)); const [VW, VH] = doc.size || [1000, 760]; -const PIX = doc.pix || 850; +const PIX = Math.round((doc.pix || 850) * SCALE); +// hgTracks offers a fixed ladder of track font sizes (hgTracks/config.c); step to the one +// closest to scaling its 8px default, so rows and labels grow with the image instead of +// staying 8px tall in a 3x-wide picture. +const TEXTSIZE = [6, 8, 10, 12, 14, 18, 24, 34].reduce((a, b) => + Math.abs(b - 8 * SCALE) < Math.abs(a - 8 * SCALE) ? b : a); +// What every hgTracks nav carries: the image width, plus the font to draw it with at scale. +const IMGVARS = `pix=${PIX}` + (SCALE > 1 ? `&textSize=${TEXTSIZE}` : ''); // FAST: iterate on the FIGURES. Everything that exists only for the video is dropped -- // the dwells, the cursor animation, the dropdown theatrics, the screen recording and the // mp4 transcode. The stills are byte-for-byte what a full run produces, and a run costs // roughly a third as long. `fast: true` in the script, DOCENT_FAST=1, or `make FAST=1 BP1`. -const FAST = !!(doc.fast || process.env.DOCENT_FAST); +// A scaled run is a figure run: at 3x the video would be a 3000px-wide recording of a tour +// nobody watches at that size, so the mp4 is skipped and only the stills are produced. Build +// the video from an unscaled run of the same script. +const FAST = !!(doc.fast || process.env.DOCENT_FAST || SCALE > 1); const PACE = FAST ? 0 : Math.round((doc.pace ?? 1.2) * 1000); // dwell after each step const SHOTHOLD = FAST ? 0 : Math.round((doc.shotHold ?? 2.2) * 1000); // extra pause at a shot // ---------- trackDb ---------- // Docent carries NO table of per-track cart variables. Such a table encodes one snapshot // of trackDb and then quietly lies when trackDb changes (this file used to pin // `clinvarMain=dense` for every `clinvar:` step, for instance). Instead ask the server for // the trackDb it is driving -- hubApi /list/tracks -- and derive what a step needs: // // * the containers above a subtrack (composite, view, superTrack) that have to be // turned on with it, and what each of those takes (a superTrack wants show/hide), // * whether trackDb leaves that subtrack UNSELECTED (`parent <c> off`), in which case // the subtrack checkbox `<name>_sel` has to come along, // * which leaf actually draws the pixels for a container name. // // Everything else -- which dropdown to open, which row to hover -- is read off the live // page. Tracks the listing doesn't know (attached hubs, custom tracks, quickLift's own // tracks on the target) fall back to a literal `name=mode`, which is all Docent could // honestly do for them anyway. const TDB_TTL = 24 * 3600 * 1000; // re-fetch a cached listing daily const TDB_CACHE = path.join(os.tmpdir(), `docent-tdb-${SERVER.replace(/[^\w.-]+/g, '_')}`); let tdbPending = null; // db -> Promise<Map|null>, once each function tdbParse(genome) { const idx = new Map(); const add = (name, o) => { const p = String(o.parent || '').trim().split(/\s+/); idx.set(name, { name, parent: p[0] || null, parentState: (p[1] || '').toLowerCase(), // on | off | a visibility | '' vis: o.visibility || null, view: o.view || null, superChild: !!o.superTrack, // member of a superTrack superTrack: false, // set below for containers children: [], }); for (const [k, v] of Object.entries(o)) if (v && typeof v === 'object' && !Array.isArray(v)) add(k, v); }; for (const [k, v] of Object.entries(genome || {})) if (v && typeof v === 'object' && !Array.isArray(v)) add(k, v); // hubApi flattens superTrack members to the top level and never lists the superTrack // itself, so synthesize the container from the `parent` field it points at. for (const n of [...idx.values()]) { if (!n.parent) continue; if (!idx.has(n.parent)) idx.set(n.parent, { name: n.parent, parent: null, parentState: '', vis: null, view: null, superChild: false, superTrack: true, children: [] }); idx.get(n.parent).children.push(n.name); } return idx; } // The cache holds the DERIVED index (a few hundred kB), not hubApi's reply (~30 MB for // hg38): same information for our purposes, ~20x less to read and parse on every run. function tdbFlatten(idx) { return { docentIndex: 1, rows: [...idx.values()].map(n => [n.name, n.parent, n.parentState, n.vis, n.view, n.superChild ? 1 : 0, n.superTrack ? 1 : 0]) }; } function tdbInflate(o) { const idx = new Map(); for (const [name, parent, parentState, vis, view, superChild, superTrack] of o.rows) idx.set(name, { name, parent, parentState, vis, view, superChild: !!superChild, superTrack: !!superTrack, children: [] }); for (const n of idx.values()) if (n.parent && idx.has(n.parent)) idx.get(n.parent).children.push(n.name); return idx; } async function tdbIndex(db) { if (!tdbPending) tdbPending = new Map(); if (tdbPending.has(db)) return tdbPending.get(db); const p = (async () => { const cache = `${TDB_CACHE}-${db}.json`; try { const st = fs.statSync(cache); if (Date.now() - st.mtimeMs < TDB_TTL) { const o = JSON.parse(fs.readFileSync(cache, 'utf8')); return o && o.docentIndex ? tdbInflate(o) : tdbParse(o); } } catch (e) {} const url = `${SERVER}/hubApi/list/tracks?genome=${enc(db)}&trackLeavesOnly=0`; try { const r = await fetch(url); if (!r.ok) throw new Error(`HTTP ${r.status}`); const j = await r.json(); const genome = j[db]; // A hub-supplied genome (an assembly hub, or quickLift's own generated target hub) // isn't in the server's trackDb listing at all -- expected, not a failure. if (!genome) { console.log(`trackDb: ${db} is not a server assembly (hub genome), ` + `so track steps there are sent as literal name=mode`); return null; } const idx = tdbParse(genome); // Write via a unique temp file + rename so parallel builds (make -j) can't read a // half-written cache. try { const tmp = `${cache}.${process.pid}.tmp`; fs.writeFileSync(tmp, JSON.stringify(tdbFlatten(idx))); fs.renameSync(tmp, cache); } catch (e) {} console.log(`trackDb: ${idx.size} tracks for ${db} from ${SERVER}/hubApi`); return idx; } catch (e) { console.warn(`trackDb: could not read ${url} (${e.message}) -- ` + `falling back to literal name=mode for every track step`); return null; } })(); tdbPending.set(db, p); return p; } const sleep = ms => new Promise(r => setTimeout(r, ms)); // A pause that exists only so a viewer can follow the video: skipped entirely in FAST. const dwell = ms => (FAST ? Promise.resolve() : sleep(ms)); // Typing is shown on screen for the video; in FAST just put the text in the box (fill() // still fires the input events the autocompletes listen for). async function typeIn(pg, sel, text) { if (FAST) await pg.fill(sel, String(text)); else await pg.type(sel, String(text), { delay: 45 }); } const enc = s => encodeURIComponent(String(s)); const state = { db: doc.db || 'hg38', position: doc.position || '', hgsid: '' }; +// ---------- SCALE: give the k-times-wider browser image the 1x amount of layout space ---------- +// hgTracks sizes the image table in the HTML it writes, so shrinking the <img> elements alone +// would leave the table 3x wider than its own contents. Zoom the table: the zoom reaches the +// images inside it, and its box goes back to the width the 1x page gives it -- 854 CSS px for +// a pix=850 run, whatever k is -- so the rest of the page is laid out exactly as at 1x while +// the image keeps all k times its pixels (one per device pixel at deviceScaleFactor: k). +// +// Installed for the whole run rather than at the shutter: the tour's own geometry -- a drag +// across the image, a mouseover on a feature -- then works in the same coordinates a 1x run +// works in, and needs no scale arithmetic of its own. +const SCALE_INIT = (k) => { + const add = () => { + if (document.getElementById('__scale')) return; + const s = document.createElement('style'); + s.id = '__scale'; + s.textContent = `#imgTbl, #chromIdeoImg, img[src*="hgtIdeo"] { zoom: ${1 / k} !important; }`; + (document.head || document.documentElement).appendChild(s); + }; + if (document.readyState === 'loading') document.addEventListener('DOMContentLoaded', add); + else add(); +}; + // ---------- animated cursor (same technique as the walkthrough-video skill's record.js) ---------- const CURSOR_INIT = () => { const add = () => { if (document.getElementById('__cur')) return; const c = document.createElement('div'); c.id = '__cur'; c.style.cssText = 'position:fixed;left:0;top:0;z-index:2147483647;pointer-events:none;width:24px;height:24px;margin-left:-3px;margin-top:-2px;filter:drop-shadow(0 1px 1px rgba(0,0,0,.4));'; c.innerHTML = '<svg width="24" height="24" viewBox="0 0 24 24"><path d="M3 2 L3 19 L7.5 14.5 L10.5 21.5 L13.5 20.2 L10.6 13.5 L17 13.5 Z" fill="#111" stroke="#fff" stroke-width="1.3"/></svg>'; document.documentElement.appendChild(c); const place = (x, y) => { c.style.transform = `translate(${x}px,${y}px)`; }; place(120, 120); document.addEventListener('mousemove', e => place(e.clientX, e.clientY), true); document.addEventListener('mousedown', e => { const r = document.createElement('div'); r.className = '__ripple'; r.style.cssText = `position:fixed;left:${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; } const T_START = Date.now(); (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, + viewport: { width: VW, height: VH }, deviceScaleFactor: SCALE, ...(FAST ? {} : { recordVideo: { dir: path.join(HERE, '.vid_' + base), size: { width: VW, height: VH } } }), }); + if (SCALE > 1) await ctx.addInitScript(SCALE_INIT, SCALE); 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) {} // Authoring aid: DOCENT_ROWS=1 logs the rows hgTracks actually drew, so "why is that // subtrack still there / why is my mouseover track not shown" is one run, not a guess. if (process.env.DOCENT_ROWS) { const rows = await page.evaluate(() => [...document.querySelectorAll('[id^="img_data_"]')].map(e => e.id.replace('img_data_', ''))).catch(() => null); if (rows) console.log(' rows:', rows.join(', ') || '(none)'); } } 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) { if (FAST) { await page.mouse.move(x, y); cur.x = x; cur.y = y; return; } 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(); if (FAST) { // no one is watching: just set it (the open/highlight is video-only) if (commit) { await loc.selectOption(val).catch(() => {}); await sleep(120); } return; } 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(() => {}); } // ---------- position-box suggestions (the gene-name path of goShow) ---------- // Rows of the open suggest menu, minus the category headings (and the trailing // "Unable to find a genome?" div, which is not an <li>). const SUGGEST_ROW = 'ul.ui-autocomplete li:not(.ui-autocomplete-category):visible'; async function suggestRows() { return await page.evaluate(() => { const rows = [...document.querySelectorAll('ul.ui-autocomplete li')] .filter(li => !li.classList.contains('ui-autocomplete-category') && li.offsetWidth > 0); return rows.map(li => { let d = null; try { if (window.jQuery) d = jQuery(li).data('ui-autocomplete-item') || null; } catch (e) {} return { text: (li.innerText || li.textContent || '').trim(), // The item's own identifier, preferred over its display label: a gene suggestion // carries geneSymbol, a genome suggestion (the Convert page's target search) // carries db/genome. `value` comes LAST because jQuery UI copies the label into // it when the item has none, which would make every row "match" its own text. sym: d ? String(d.geneSymbol || d.db || d.genome || d.value || '') : '', recent: !!(d && d.displayCategory === 'Recent'), // a previously-visited position }; }); }); } // Choose the suggestion row for `term`, waiting out the hgSuggest ajax. Two traps this // handles: the "Recent" positions render INSTANTLY, so a plain "menu is up" wait picks a // recent position instead of the gene; and when the real suggestions arrive the menu is // re-rendered, so a row chosen too early is gone by the time we click it. So: poll until // a row actually matches AND the menu has stopped changing. `want` (goShow's `pick:`) // overrides the match, for a term with several sensible hits. Returns {index, text} into // the SUGGEST_ROW set, or null if nothing ever matched. async function pickSuggest(term, want, ms = 8000) { const t0 = Date.now(); const low = s => String(s).toLowerCase(); const demote = (s, r) => (s ? s - (r.recent ? 0.5 : 0) : 0); // a real hit beats a recent one // A term that appears as a whole token in the row text counts as a real match -- an // accession sits in parentheses ("human (HG02148.mat 2021) (GCA_018471535.1)"), so // neither an id compare nor startsWith would catch it. const tokenRe = new RegExp(`(^|[^A-Za-z0-9_.])${String(term).replace(/[.*+?^${}()|[\]\\]/g, '\\$&')}([^A-Za-z0-9_.]|$)`, 'i'); const scoreTerm = r => demote( low(r.sym) === low(term) ? 3 : // the item's own id low(r.text).startsWith(low(term)) ? 2 : // label starts with the term tokenRe.test(r.text) ? 2 : // term appears as a token low(r.text).includes(low(term)) ? 1 : 0, r); const scoreWant = r => demote(want && low(r.text).includes(low(want)) ? 3 : 0, r); const pickBest = (rows, fn) => { let bi = -1, bs = 0; rows.forEach((r, i) => { const s = fn(r); if (s > bs) { bs = s; bi = i; } }); return bi < 0 ? null : { index: bi, text: rows[bi].text, score: bs }; }; const deadline = Date.now() + ms; let prev = null, byTerm = null, byWant = null; while (Date.now() < deadline) { const rows = await suggestRows(); const sig = JSON.stringify(rows.map(r => r.text)); // Same authoring aid as the drawn-row dump: shows what the menu offered and what // identifier each row carries, which is how you tell why a pick went elsewhere. if (process.env.DOCENT_ROWS && sig !== prev) console.log(' suggest:', JSON.stringify(rows)); byTerm = pickBest(rows, scoreTerm) || byTerm; byWant = want ? (pickBest(rows, scoreWant) || byWant) : null; const b = want ? byWant : byTerm; // matched, and the menu settled if (b && b.score >= 2 && sig === prev) return { ...b, ms: Date.now() - t0 }; prev = sig; await sleep(400); } // `pick:` that matches nothing shouldn't throw away the gene: fall back to the plain // term match (and say so) rather than skipping the menu and submitting raw text. if (want && !byWant && byTerm) console.warn(`goShow ${term}: pick "${want}" matched no suggestion, using "${byTerm.text}"`); const out = want ? (byWant || byTerm) : byTerm; return out ? { ...out, ms: Date.now() - t0, timedOut: true } : null; } // ---------- what a `track:` step has to send, per trackDb ---------- // Cart variables that put `name` in `mode`, as [key, value] pairs: the track itself, its // subtrack checkbox if trackDb leaves it unselected, and every container above it -- a // composite or view takes the mode, a superTrack takes show. Nothing is pushed DOWNWARD: // a container's visibility reaches its selected children on its own (`clinvar=pack` draws // clinvarMain/clinvarCnv/clinvarSubLolly, `dbSnp155Composite=pack` draws dbSnp155Common), // which is why the author only has to name deviations from trackDb. A name trackDb doesn't // know (hub, custom, quickLift target) gets a literal `name=mode`. async function visVars(name, mode) { const idx = await tdbIndex(state.db); const n = idx && idx.get(name); if (!n) return [[name, mode]]; if (n.superTrack && !['show', 'hide'].includes(mode)) { console.warn(`track ${name}: superTrack container takes show/hide, not "${mode}" -- using show`); mode = 'show'; } const out = [[name, mode]]; // A subtrack of a composite is governed by its CHECKBOX, not its visibility: when the // container's own vis var is in the same request, hgTracks reshapes the composite and a // bare `clinvarCnv=hide` is dropped (the cart keeps clinvarCnv_sel=1 and the row still // draws). So state the selection explicitly in both directions. Views are containers, // not selectable rows, so they are left out of this. const parent = n.parent ? idx.get(n.parent) : null; if (parent && !parent.superTrack && !n.children.length) out.push([`${name}_sel`, mode === 'hide' ? '0' : '1']); // Hiding a subtrack says NOTHING about its container: propagating `hide` upward would // turn the whole composite off (`{clinvar: pack, clinvarCnv: hide}` would end in // clinvar=hide and no ClinVar at all). if (mode === 'hide') return out; for (let p = n.parent; p; ) { const pn = idx.get(p); out.push([p, pn && pn.superTrack ? 'show' : mode]); p = pn ? pn.parent : null; } return out; } // Leaf descendants of a container, in trackDb order (a container draws no pixels of its // own, so a `mouseover:`/`click:` naming one has to be resolved to a row that does). async function tdbLeaves(name) { const idx = await tdbIndex(state.db); const n = idx && idx.get(name); if (!n || !n.children.length) return []; const out = []; const walk = k => { const c = idx.get(k); if (!c || !c.children.length) out.push(k); else c.children.forEach(walk); }; n.children.forEach(walk); return out; } // The track-controls dropdown to open for the visible gesture. Composite children have no // dropdown of their own (the container carries it), so walk up until the DOM has one. async function ctrlSelect(name) { const idx = await tdbIndex(state.db); for (let k = name; k; ) { const sel = `select[name="${k}"]`; if (await page.locator(sel).count()) return sel; const n = idx && idx.get(k); k = n ? n.parent : null; } return null; } async function shot(name) { const p = path.join(STILLDIR, name + '.png'); // Drop any click ripple still fading: it reads as a red blob over whatever was just // clicked. It belongs to the video, not to a figure. await page.evaluate(() => document.querySelectorAll('.__ripple').forEach(e => e.remove())).catch(() => {}); // 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 if (await page.locator('#imgTbl').count()) { await page.locator('#imgTbl').screenshot({ path: p }); } else { // Not a tracks page (hgc detail page, an external page a link led to, ...). An element // shot of <main> would run the whole scrolling page -- thousands of pixels tall and // unusable as a figure. Capture the viewport only, i.e. the top of the page. await page.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`. // A container draws nothing itself, so if the name given is one, fall through to the // leaves trackDb lists under it and take the first that is actually on the page. async function trackBox(t) { const cands = [t, ...await tdbLeaves(t)]; let key = null; for (const c of cands) { 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_', '') : null; }, c); if (key) { if (c !== t) console.log(`track ${t}: drawn by "${c}"`); break; } } if (!key) throw new Error(`track "${t}" not shown (no #img_data_ for ${cands.join(', ')})`); const img = await page.locator(`#img_data_${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 }; + // Everything hgTracks reports about the image -- map-box coords, mouseOver spans, + // insideX -- is in the pixels of the image the SERVER drew, which is not the size the + // page shows it at when the image is scaled (SCALE). imgPx is that ratio, so those + // numbers can be turned into page coordinates: 1 normally, 1/SCALE for a print render. + const imgPx = await page.evaluate(k => { + const im = document.getElementById('img_data_' + k); + return im && im.naturalWidth ? im.getBoundingClientRect().width / im.naturalWidth : 1; + }, key); + return { key, img, row, imgPx: imgPx || 1 }; } // 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 { key, img, row, imgPx } = 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') || a.getAttribute('mouseoverText') || ''; 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="#${nm}"]`); const r = im ? im.getBoundingClientRect() : null; const ox = r ? r.left : imgBox.x, oy = r ? r.top : imgBox.y; - const cx = ox + (c[0] + c[2]) / 2, cy = oy + (c[1] + c[3]) / 2; + // coords are in the drawn image's own pixels; s converts them to page pixels + const s = (r && im.naturalWidth) ? r.width / im.naturalWidth : 1; + const cx = ox + s * (c[0] + c[2]) / 2, cy = oy + s * (c[1] + c[3]) / 2; // The tooltip's own text, so the hover can wait for THIS item's tooltip rather than // for any tooltip at all (see mouseover()). Rendered exactly the way the tooltip // renders it -- innerHTML then textContent -- because the attribute holds markup AND // undecoded entities (`<b>`, `★`) that getAttribute hands back literally. const tmp = document.createElement('div'); tmp.innerHTML = title; const tip = (tmp.textContent || '').replace(/\s+/g, ' ').trim(); cands.push({ cx, cy, href, tip, inBand: cy >= band.top - 1 && cy <= band.bot + 1 }); } const inBand = cands.filter(h => h.inBand); const pick = (inBand[0] || cands[0]) || null; return pick && { ...pick, n: cands.length, nBand: inBand.length, all: cands.map(c => Math.round(c.cx)) }; }, { want: String(want), titleOnly: !!titleOnly, band, imgBox: img }); if (area) { if (process.env.DOCENT_ROWS) console.log(` item "${want}" in ${t}: ${area.n} map box(es) match (${area.nBand} in row), ` + `centers x=[${area.all}] -> hovering (${Math.round(area.cx)},${Math.round(area.cy)})` + (area.tip ? `, expecting tip "${area.tip.slice(0, 40)}"` : '')); return { x: area.cx, y: area.cy, href: area.href, tip: area.tip }; } 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 }; + if (!span) { + // Say WHAT is there instead. An item name that has gone missing is usually a track + // whose items depend on the pixel width -- a print render (SCALE) draws a wider image, + // so features hgTracks merged into one box at screen width come apart into several + // with names of their own -- and the fix is to pick from the names that do exist. + const near = await page.evaluate(({ band }) => { + const out = []; + for (const a of document.querySelectorAll('map[name^="map_"] area')) { + const c = (a.getAttribute('coords') || '').split(',').map(Number); + if (c.length < 4) continue; + const m = a.closest('map'), nm = m && m.getAttribute('name'); + const im = nm && document.querySelector(`img[usemap="#${nm}"]`); + if (!im) continue; + const r = im.getBoundingClientRect(); + const s = im.naturalWidth ? r.width / im.naturalWidth : 1; + const cy = r.top + s * (c[1] + c[3]) / 2; + if (cy < band.top - 1 || cy > band.bot + 1) continue; + const i = (a.getAttribute('href') || '').match(/[?&]i=([^&]+)/); + if (i) out.push(decodeURIComponent(i[1])); + } + return out; + }, { band }).catch(() => []); + const win = await page.evaluate(() => { + try { return `${hgTracks.chromName}:${hgTracks.winStart}-${hgTracks.winEnd}`; } + catch (_) { return '?'; } + }).catch(() => '?'); + const show = process.env.DOCENT_ROWS ? near : near.slice(0, 12); + throw new Error(`item "${want}" not found in track "${t}" (searched map-box areas + ` + + `mouseOver spans). Window ${win}.${near.length ? ` In that row: ${show.join(', ')}` + + `${show.length < near.length ? `, ... (${near.length} total; DOCENT_ROWS=1 for all)` : ''}` + : ''}`); + } + return { x: img.x + imgPx * (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; } }); + const { img, row, imgPx } = await trackBox(t); + const insideX = imgPx * await page.evaluate(() => { try { return hgTracks.insideX || 0; } catch (_) { return 0; } }); let x; - if (o.x != null) x = img.x + insideX + Number(o.x); + if (o.x != null) x = img.x + insideX + imgPx * 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 spot = (want != null) ? await itemXY(t, want, o.title != null && o.item == null && o.value == null) : await posXY(t, o); const { x, y } = spot; // Raise a FRESH tooltip for THIS item, and be sure it IS this item's. The browser shows // a tooltip on MOUSEENTER after a 500ms delay and hides it 500ms after mouseleave // (hg/js/utils.js addMouseover), so while the cursor glides in it crosses other items // and any of THEIR tooltips can still be on screen when we arrive -- an Alignment // Differences item recorded as "identical" (the neighbouring aligned block, lingering in // its grace period) when the item under the cursor reads "mismatch C->T". Waiting for // "some tooltip is visible" is therefore not enough: when we know the item's own text // (from its map box) we wait for exactly that. const tipHtml = () => page.evaluate(() => { const c = document.getElementById('mouseoverContainer'); if (!c || !c.offsetWidth) return null; const st = getComputedStyle(c); return (st.display === 'none' || st.visibility === 'hidden') ? null : c.innerHTML; }); const prevTip = await tipHtml(); await page.mouse.move(2, y); cur.x = 2; cur.y = y; if (prevTip) await page.waitForFunction(() => { const c = document.getElementById('mouseoverContainer'); if (!c || !c.offsetWidth) return true; const st = getComputedStyle(c); return st.display === 'none' || st.visibility === 'hidden'; }, null, { timeout: 2000 }).catch(() => {}); await sleep(60); 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); const shown = () => page.evaluate(() => { const c = document.getElementById('mouseoverContainer'); if (!c || !c.offsetWidth) return null; const st = getComputedStyle(c); if (st.display === 'none' || st.visibility === 'hidden') return null; return (c.textContent || '').replace(/\s+/g, ' ').trim(); }); const wantTip = spot.tip || null; if (wantTip) { // The item's own tooltip, or nothing. A neighbour's tooltip lingering from the glide // fails this test, so we keep waiting until the 500ms show timer fires for OUR item. // Compared with ALL whitespace removed: the title's markup (`<b>rsID</b>: ...`, `<br>`) // leaves no whitespace at all in textContent, so any tag-to-space normalisation would // never match and the wait would just burn its timeout on a tooltip that was right. await page.waitForFunction(w => { const c = document.getElementById('mouseoverContainer'); if (!c || !c.offsetWidth) return false; const st = getComputedStyle(c); if (st.display === 'none' || st.visibility === 'hidden') return false; const flat = z => z.replace(/\s+/g, ''); // A distinctive PREFIX, not the whole string: the head of a mouseOver carries the // item's identity (its name/HGVS), while the tail can render differently from the // title it came from (entities, stars, a max-width span). Short tips match whole. return flat(c.textContent || '').includes(flat(w).slice(0, 60)); }, wantTip, { timeout: 4000 }).catch(() => {}); const flat = z => (z || '').replace(/\s+/g, ''); if (process.env.DOCENT_ROWS && !flat(await shown()).includes(flat(wantTip).slice(0, 60))) console.warn(` WARNING: mouseover ${t} "${want}": tooltip never showed its own text\n` + ` want: ${JSON.stringify(flat(wantTip).slice(0, 70))}\n` + ` got : ${JSON.stringify(flat(await shown()).slice(0, 70))}`); } else { await page.waitForFunction(prev => { const c = document.getElementById('mouseoverContainer'); if (!c || !c.offsetWidth) return false; const st = getComputedStyle(c); if (st.display === 'none' || st.visibility === 'hidden') return false; return prev == null || c.innerHTML !== prev; }, prevTip, { timeout: 3000 }).catch(() => {}); } // A POSITIONAL hover has no expected text to wait for, so the best it can do is let the // tooltip settle: the content stops changing once the cursor is parked, so sample until // two reads agree. (A pinned positional hover therefore still records whatever is under // the point -- `frac: 0.5` can land between two features and report the block they sit // in. Name the item when the figure depends on which tooltip it is.) if (!wantTip) { let settled = await tipHtml(); for (let i = 0; i < 15; i++) { await sleep(80); const now = await tipHtml(); if (now && now === settled) break; settled = now; } } if (process.env.DOCENT_ROWS) console.log(` tip at (${Math.round(x)},${Math.round(y)}): ` + JSON.stringify(((await shown()) || '').slice(0, 90))); // 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); if (!FAST) 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 }); + const ctx2 = await browser.newContext({ viewport: { width: VW, height: VH }, deviceScaleFactor: SCALE }); + if (SCALE > 1) await ctx2.addInitScript(SCALE_INIT, SCALE); 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: ${pinnedTips.length})`); pinnedTips.length = 0; // consume the set } // Shift+drag across the track image to open the browser's own drag-select dialog // ("Zoom In / Single Highlight / ..."), then act on it. The usual form gives one // genomic region and zooms: drag: chr7:155,806,100-155,806,557 // Any other action needs the map form, which is also how you pass shot:/track: // drag: {range: "chr7:155,806,100-155,806,557", then: highlight} // Endpoints that are not genomic coords use a fraction // across the view (fromFrac:/toFrac:) or a raw pixel (fromX:/toX:) instead. // Optional `track:` picks the row the drag runs over (y); default is the middle of // the image. `shot:` captures the open dialog (e.g. the Figure 1A drag-select box). // `then:` = zoom (default, clicks Zoom In) | highlight (Single Highlight) | cancel // (Escape, leaves the view unchanged). async function drag(o) { // A bare string is the region; `range:` is the same thing with room for other // keys. Both expand to the from:/to: endpoints the rest of this function uses. if (typeof o === 'string') o = { range: o }; o = o || {}; if (o.range != null) { const m = String(o.range).match(/^\s*(.+):([\d,]+)\s*-\s*([\d,]+)\s*$/); if (!m) throw new Error(`drag: range "${o.range}" is not chrom:start-end`); o = Object.assign({}, o, { from: `${m[1]}:${m[2]}`, to: `${m[1]}:${m[3]}` }); } 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; } }); + // insideX and any px: endpoint are in the drawn image's pixels; imgPx converts them to + // page pixels (1 normally, 1/SCALE when the image is scaled for print). + const imgPx = await page.evaluate(() => { + const im = document.querySelector('img[id^="img_data_"]'); + return im && im.naturalWidth ? im.getBoundingClientRect().width / im.naturalWidth : 1; + }) || 1; + const insideX = imgPx * 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); + if (px != null) return img.x + imgPx * 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 row = await trackBox(o.track).then(b => b.row).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} ${m.t}`)); } return matches[0].v; } async function convert(o) { o = o || {}; // `shot:` here can name up to three moments of the Convert page, none of which any // other verb can reach (after Submit the tour is already on the results page): // shot: convert_filled -- just before Submit (the common one) // shot: {opened: a, filled: b, result: c} // opened the page as it comes up, nothing chosen yet // filled target searched for, QuickLift/Hide-defaults set -- ready to Submit // result the conversion result page (the coordinate link `open: lift` clicks) const shots = (o.shot == null) ? {} : (typeof o.shot === 'string' ? { filled: o.shot } : o.shot); for (const k of Object.keys(shots)) if (!['opened', 'filled', 'result'].includes(k)) console.warn(`convert shot: unknown moment "${k}" (use opened, filled or result)`); try { await glideTo('#view'); await page.hover('#view'); await dwell(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=${enc(state.position)}`); await page.waitForSelector('#hglft_toDbSelect'); } if (shots.opened) await shot(shots.opened); // Find the target the way a user does: TYPE it into the Convert page's own "Search for // target genome" bar and click the suggestion (the species autocomplete takes an // accession or a name, and is already filtered to assemblies hg38 can lift to). So the // string the script names is visibly searched for on screen, not silently selected. // `search:` overrides what gets typed; `pick:` disambiguates the menu. const term = o.search != null ? o.search : o.to; let searched = false; if (term != null && await page.locator('#toGenomeSearch:visible').count()) { await glideTo('#toGenomeSearch'); await page.click('#toGenomeSearch'); await dwell(160); await page.fill('#toGenomeSearch', ''); const label0 = await page.locator('#toGenomeLabel').textContent().catch(() => ''); await typeIn(page, '#toGenomeSearch', term); await dwell(300); const hit = await pickSuggest(String(term), o.pick); if (hit) { console.log(`convert: searched "${term}" -> "${hit.text}"` + (hit.timedOut ? ` (no strong match, waited ${hit.ms}ms)` : '')); const li = page.locator(SUGGEST_ROW).nth(hit.index); const b = await li.boundingBox().catch(() => null); if (b) await glide(b.x + b.width / 2, b.y + b.height / 2); await dwell(220); await li.click(); // Picking a genome repopulates the Assembly dropdown (ajax) and rewrites the hidden // toDb field. Wait for the "Selected:" label to actually change instead of guessing // a duration -- right on a fast server, still correct on a slow one. await page.waitForFunction(b0 => { const el = document.getElementById('toGenomeLabel'); return el && (el.textContent || '') !== b0; }, label0, { timeout: 5000 }).catch(() => {}); await dwell(300); searched = true; } else { console.warn(`convert: "${term}" matched nothing in the target-genome search`); } } // The Assembly dropdown is what actually gets submitted, so confirm it landed on the // requested assembly; open it visibly only if the search didn't get us there. const val = await resolveTarget(o.to); const landed = await page.locator('#hglft_toDbSelect').inputValue().catch(() => null); if (!searched || landed !== val) { if (searched) console.log(`convert: Assembly dropdown is on "${landed}", picking ${val}`); await openSelectVisible('#hglft_toDbSelect', val); } await page.waitForSelector('#doQuickLift', { timeout: 8000 }).catch(() => {}); await dwell(400); if (o.quicklift !== false) await checkGlide('#doQuickLift', true); await checkGlide('#hideTracksOnConvert', o.hideDefaults !== false); // reverts on assembly change -> set explicitly await dwell(300); if (shots.filled) await shot(shots.filled); await clickGlide('#hglft_doConvert'); await page.waitForLoadState('load'); await captureState(); if (shots.result) await shot(shots.result); } // On the "Hub Connect Successful" page, click the "Open:" link for `db` so the demo // ends on the browser with the hub loaded. The links look like // hgTracks?hubUrl=...&db=<genome>&position=lastDbPos (or &genome=<genome>). async function openHubAssembly(db) { const sel = await page.evaluate((db) => { const esc = db.replace(/[.*+?^${}()|[\]\\]/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=${PIX}`); } + else { await nav(`/cgi-bin/hgTracks?db=${state.db}&position=${enc(arg)}&${IMGVARS}`); } await captureState(); break; case 'goShow': { // DEMONSTRATE the position change through the UI (vs. `go:` which navs straight to // the new position): glide to the position box, clear it, type on screen, then let // the page take it from there -- "Search" (#goButton) on hgTracks, the arrow // (.jwGoButtonContainer) on hgGateway, so one verb covers either page. // // Takes a POSITION or a GENE NAME (or any search term the box accepts: HGVS, an // accession, ...). A gene name goes through the browser's own suggestion menu, the // way a user does it: wait for the menu, then click the matching item -- hgTracks' // handler sets the position from that item and submits, so we land on the gene // instead of the search-results page. `pick:` chooses among the suggestions when // the term is ambiguous (substring of the menu row); default is an exact symbol // match, else the first row. // // goShow: BRCA1 // goShow: {gene: SHH, shot: source} // goShow: {position: "chr7:155,799,529-155,812,871", shot: source} // goShow: {gene: BRCA1, pick: "NM_007294", shot: source} const o = (typeof arg === 'string') ? { position: arg } : (arg || {}); const pos = [o.position, o.pos, o.gene, o.search].find(v => v != null && v !== ''); if (pos == null) { console.warn('goShow: no position or gene given'); break; } const term = String(pos).trim(); // A coordinate has no suggestions to wait on; anything else is a search term. const isPos = /^[\w.|-]+:[\d,]+(-[\d,]+)?$/.test(term); if (!await page.locator('#positionInput:visible').count()) throw new Error('goShow: no position box on this page (need hgTracks or hgGateway) -- ' + page.url()); await glideTo('#positionInput'); await page.click('#positionInput'); await dwell(160); await page.fill('#positionInput', ''); // clear the old position await dwell(200); await typeIn(page, '#positionInput', term); // visible typing await dwell(450); pinnedTips.length = 0; // new view, old tips don't apply let done = null; if (!isPos) { const hit = await pickSuggest(term, o.pick != null ? o.pick : o.match); if (hit) { console.log(`goShow ${term}: suggestion "${hit.text}"` + (hit.timedOut ? ` (no strong match, waited ${hit.ms}ms)` : '')); // Address the row by index at click time (a late re-render replaces the <li> // elements, so a handle or a marker attribute taken earlier goes stale). const li = page.locator(SUGGEST_ROW).nth(hit.index); // Arm the nav wait BEFORE the click (the page's own handler submits the form for // us), and wait on 'commit' so we can tell "navigated" from "only filled the box". const committed = page.waitForNavigation({ waitUntil: 'commit', timeout: 15000 }).catch(() => null); const b = await li.boundingBox().catch(() => null); if (b) await glide(b.x + b.width / 2, b.y + b.height / 2); await sleep(220); await li.click(); done = await committed; if (done) await page.waitForLoadState('load').catch(() => {}); } else { console.warn(`goShow ${term}: no suggestion matched, submitting the term as typed`); } } // Coordinate, no suggestions, or hgGateway (where picking a suggestion only fills // the box): click the page's own go button. Arm the nav wait BEFORE the click -- on // hgTracks the OLD page already has an #imgTbl, so waiting on the selector alone // returns instantly and a following shot races the reload ("Cannot find context // with specified id"). if (!done) { const navDone = page.waitForNavigation({ waitUntil: 'load', timeout: 30000 }).catch(() => {}); await clickGlide((await page.locator('#goButton').count()) ? '#goButton' : '.jwGoButtonContainer'); await navDone; } // A unique hit lands on the track image; a term with no suggestion and several // matches lands on the search-results page instead, which has no #imgTbl -- that's // legal, the script can `click` a result from there. await page.waitForSelector('#imgTbl', { timeout: 15000 }).catch(() => {}); await captureState(); await page.mouse.move(cur.x, cur.y); // re-show the cursor overlay if (o.shot) { await shot(o.shot); return; } break; } case 'hide': if (arg === 'all' || arg === true) { await clickGlide('#hgt\\.hideAll'); await page.waitForSelector('#imgTbl'); } break; case 'track': { let entries = Object.entries(arg); const isKidHide = ([, mode]) => String(mode).toLowerCase() === 'hidekids'; // What the author spelled out AS A VISIBILITY. A `hideKids` container is deliberately // NOT in here: it names no mode of its own, so it must not suppress the container // variable derived from a child below it (`pubtator: pack` is what turns varsInPubs on). const named = new Set(entries.filter(e => !isKidHide(e)).map(([n]) => n)); const idx = await tdbIndex(state.db); // `hideKids` is not a visibility -- it is "hide everything under this container", so // that a child named alongside it is left the only one drawn. A superTrack needs it: // unlike a composite, its own mode does NOT reach its children, so every child comes // up at its own trackDb visibility and an earlier `hide: all` does not stick // (`{varsInPubs: show}` alone draws all eight of its members). The expansion skips any // child the step names itself, and runs in a round of its own AFTER the rest, because // a subtrack hide travelling in the same request as its container can be dropped by // the cart (#37953) -- so the container goes on first and the hides follow. const kidHides = []; for (const e of entries.filter(isKidHide)) { const leaves = (await tdbLeaves(e[0])).filter(k => !named.has(k)); if (!leaves.length) console.warn(`track ${e[0]}: hideKids -- trackDb gives it no children to hide`); for (const k of leaves) kidHides.push([k, 'hide']); } entries = entries.filter(e => !isKidHide(e)); // Visible gesture first: drive the real track-controls dropdowns so the mouse is // seen turning the tracks on. State is still applied by the nav()s below (which // carry the container/checkbox vars too), so these opens are non-committing. if (doc.trackAnim !== false) for (const [name, mode] of entries) { const csel = await ctrlSelect(name); if (csel) await openSelectVisible(csel, mode, 6, false); } // hgTracks RESHAPES a composite when its container visibility changes, and that wipes // per-subtrack overrides arriving in the same request (`clinvar=pack&clinvarCnv=hide` // leaves clinvarCnv_sel=1 and the CNV row still drawn). So a step that names both a // composite and something under it is applied in rounds -- container first, then the // deviations -- which is exactly what writing them as two steps does. superTracks // don't reshape, so they don't force a round. const rounds = new Map(); for (const e of entries) { let d = 0; for (let k = e[0]; ;) { const n = idx && idx.get(k); if (!n || !n.parent) break; const p = idx.get(n.parent); if (named.has(n.parent) && !(p && p.superTrack)) d++; k = n.parent; } if (!rounds.has(d)) rounds.set(d, []); rounds.get(d).push(e); } if (kidHides.length) rounds.set(Number.MAX_SAFE_INTEGER, kidHides); for (const d of [...rounds.keys()].sort((a, b) => a - b)) { const vars = new Map(); for (const [name, mode] of rounds.get(d)) // A derived variable never overrides one the step names itself, whatever the // order: `{clinvar: pack, clinvarCnv: hide}` keeps clinvar=pack. for (const [k, v] of await visVars(name, mode)) if (k === name || !named.has(k)) vars.set(k, v); const parts = [...vars].map(([k, v]) => `${k}=${v}`); console.log('track:', parts.join(' ')); // what trackDb turned the step into - await nav(`/cgi-bin/hgTracks?db=${state.db}&position=${enc(state.position)}&${parts.join('&')}&pix=${PIX}`); + await nav(`/cgi-bin/hgTracks?db=${state.db}&position=${enc(state.position)}&${parts.join('&')}&${IMGVARS}`); } break; } case 'convert': await convert(arg); break; case 'hub': { // Attach a track hub by URL: hgTracks?hubUrl=... connects the hub and makes its // tracks available at their hub-declared visibility. Follow with `track:` to turn // specific ones on. Accepts a bare URL or {url:, db:, position:}. const o = (typeof arg === 'string') ? { url: arg } : (arg || {}); if (!o.url) { console.warn('hub: no url given'); break; } const db = o.db || state.db; const pos = o.position != null ? o.position : state.position; const parts = [`db=${db}`, `hubUrl=${enc(o.url)}`]; if (pos) parts.push(`position=${enc(pos)}`); - parts.push(`pix=${PIX}`); + parts.push(IMGVARS); await nav(`/cgi-bin/hgTracks?${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 'zoom': { + const btn = (arg === 'in') ? '#hgt\\.in2' : '#hgt\\.out2'; + const was = await page.evaluate(() => { + try { return `${hgTracks.winStart}-${hgTracks.winEnd}`; } catch (_) { return ''; } + }); + await clickGlide(btn); + await page.waitForSelector('#imgTbl'); + // The zoom buttons redraw the image in place (ajax), so #imgTbl never went away and + // waiting for it proves nothing: the next step can read the OLD view's map boxes and + // report an item "not found" that simply is not in view yet. Wait for the window to + // change instead. Until FAST there was always a dwell here hiding this. + if (was) await page.waitForFunction( + w => { try { return `${hgTracks.winStart}-${hgTracks.winEnd}` !== w; } catch (_) { return false; } }, + was, { timeout: 15000 }) + .catch(() => console.warn(`zoom ${arg}: window still ${was} after 15s`)); + await captureState(); + 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 (SCALE > 1) + console.log(`scale: ${SCALE}x -- pix=${PIX}, textSize=${TEXTSIZE}, dpr=${SCALE} at ${VW}x${VH}, ` + + `stills only (no mp4) -> ${STILLDIR}`); if (doc.reset) await page.goto(absurl('/cgi-bin/cartReset?skipLs=1'), { waitUntil: 'domcontentloaded' }); const steps = doc.steps || []; const timing = []; for (let i = 0; i < steps.length; i++) { const s = norm(steps[i]); const t0 = Date.now(); 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); } timing.push({ n: i + 1, verb: s.verb, ms: Date.now() - t0 }); } await page.waitForTimeout(300); await ctx.close(); await browser.close(); // Where did the wall clock go? DOCENT_TIME=1 prints the per-step table -- the dwells // (pace/shotHold) and the page loads dominate, which is what FAST=1 trims. if (process.env.DOCENT_TIME) { const tot = timing.reduce((a, t) => a + t.ms, 0); console.log(`--- steps: ${(tot / 1000).toFixed(1)}s total`); for (const t of [...timing].sort((a, b) => b.ms - a.ms)) console.log(` ${(t.ms / 1000).toFixed(1)}s step ${t.n} ${t.verb}`); } if (FAST) { console.log('DONE (fast: stills only, no mp4) -> stills in', STILLDIR, `| ${((Date.now() - T_START) / 1000).toFixed(0)}s`); return; } const tVid = Date.now(); // 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 }); if (process.env.DOCENT_TIME) console.log(`--- mp4 transcode: ${((Date.now() - tVid) / 1000).toFixed(1)}s`); console.log('DONE ->', OUTMP4, '| stills in', STILLDIR, `| ${((Date.now() - T_START) / 1000).toFixed(0)}s`); })().catch(e => { console.error(e); process.exit(1); });