@jbrowse/capture 4.3.0

package/LICENSE

@@ -0,0 +1,201 @@
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package/README.md

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+# @jbrowse/capture
+
+Drive a live JBrowse 2 instance with Puppeteer and screenshot it **once it has
+actually finished rendering**.
+
+```bash
+npx @jbrowse/capture --hub hg38 --loc BRCA1 \
+  --track hg38-ncbiRefSeqCurated --track hg38-phyloP100way -o brca1.png
+```
+
+`--hub` names an assembly on [genomes.jbrowse.org](https://genomes.jbrowse.org),
+which hosts a ready-made JBrowse config per UCSC and GenArk genome, and `--loc`
+takes a gene name because those configs ship a text index.
+
+## Knowing when JBrowse has finished rendering
+
+Knowing when a genome browser is done is the entire problem. JBrowse loads its
+config, builds a session, resolves an assembly, fetches each track, and then
+draws to a canvas — and a screenshot taken at any point before the last step is
+a picture of an empty browser that looks like a successful run.
+
+Every readiness signal JBrowse publishes is **negative**: no loading overlay, no
+display in its loading phase, no unpainted canvas. All of them therefore pass on
+a page whose JavaScript has not started yet. Measured against
+`jbrowse.org/code/jb2/latest`:
+
+- `networkidle2` resolves at ~350ms
+- the session appears at ~880ms
+- the assembly and tracks land at ~2500ms
+- the loading overlay only goes up _after that_
+
+A wait chain built from those signals alone finishes in under a second and
+reports success.
+
+So this package puts a **positive gate** in front of them, read off the live MST
+session model that jbrowse-web publishes as `window.JBrowseSession`: the session
+exists, its views are initialized, and the assembly and trackIds you asked for
+are the ones actually open. A config URL that 404s, a trackId the config does
+not define, and an assembly name that does not match all fail there, loudly.
+
+## Library
+
+```js
+import { captureJBrowse, openJBrowse } from '@jbrowse/capture'
+
+// one call: launch, wait, shoot, close
+const { pending, paintContract } = await captureJBrowse({
+  hub: 'hg38',
+  loc: 'BRCA1',
+  tracks: ['hg38-ncbiRefSeqCurated'],
+  out: 'brca1.png',
+})
+
+// or keep the page, to click things and read state back
+const { browser, page } = await openJBrowse({ hub: 'mm39', loc: 'Sox2' })
+const tracks = await page.evaluate(
+  () => window.JBrowseSession.views[0].tracks.length,
+)
+await browser.close()
+```
+
+Two waits, depending on what you did:
+
+- **`waitForJBrowseReady(page)`** is the wait on its own, for a page you
+  navigated yourself. The individual stages (`waitForSession`,
+  `waitForLoadingComplete`, `waitForDisplaysDone`, `waitForQuiescent`, ...) are
+  exported too, and each one documents what it can and cannot tell you.
+- **`waitForAppSettled(page)`** is the wait after you CLICK something. A page
+  that is loading starts out `loading` and the transition into `ready` is it
+  finishing; a page you just clicked is already `ready` and stays that way until
+  the click's work registers, so waiting for `ready` there returns on the
+  pre-click frame. `waitForAppSettled` requires it to hold.
+
+## Timeouts and unsettled waits
+
+Puppeteer waits are usually written `.catch(() => {})` so a slow page is not
+failed for being slow. The cost is that "everything settled" and "we gave up"
+become the same `void` — the run ends with an image and an exit code of 0 either
+way, which is the vacuous-gate problem again, one step later.
+
+Here every stage reports its outcome, and an unsettled one throws by default,
+naming the gate:
+
+```
+gave up waiting after 2000ms: the loading overlay never cleared (a track fetch
+never finished). Raise the timeout if the page is merely slow; if it never
+finishes, open the same URL in a browser — this gate has no content to fall
+through to.
+```
+
+`allowUnsettled` (`--allowUnsettled`) takes the frame as it stands instead, and
+still tells you what did not settle.
+
+## Reading the result
+
+Three fields on a successful capture:
+
+- **`unsettled`** — stages that hit their timeout. Empty unless you asked to
+  proceed anyway.
+- **`pending`** — displays still reporting unpainted when the shutter fired. A
+  display can return to pending after its stage passed, so this is a separate
+  question from `unsettled`.
+- **`paintContract`** — whether this JBrowse build publishes the per-display
+  paint attributes at all. It does not on the current released build, which is
+  what every genomes.jbrowse.org link opens; there, `pending: []` means "cannot
+  tell", not "all done", and the CLI says so. A page with no tracks open reports
+  true — there is nothing to measure, which is not the same as being unable to.
+
+## CLI
+
+`jb2capture --help` for the full list. Also:
+
+```bash
+jb2capture list hg38 conservation   # trackIds matching a filter
+jb2capture url --hub hg38 --loc BRCA1   # just print the link, no browser
+```
+
+## See also
+
+- [@jbrowse/img](https://www.npmjs.com/package/@jbrowse/img) renders SVG/PNG
+  with no browser at all, via server-side React. Prefer it for a static figure;
+  use this when you need the real app — canvas and WebGPU rendering, dialogs,
+  menus, or state read back out of a running session.
+- [Using JBrowse with AI agents](https://jbrowse.org/jb2/docs/agents/)

package/esm/args.d.ts

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+export interface ParsedArgs {
+    hub?: string;
+    config?: string;
+    assembly?: string;
+    loc?: string;
+    tracks: string[];
+    session?: string;
+    sessionName?: string;
+    instance?: string;
+    out?: string;
+    width?: number;
+    height?: number;
+    scale?: number;
+    timeout?: number;
+    settle?: number;
+    fullPage: boolean;
+    headed: boolean;
+    verbose: boolean;
+    help: boolean;
+    allowUnsettled: boolean;
+}
+/**
+ * Parse `jb2capture` flags. Split from the binary so the accepted shapes are
+ * unit-testable without launching a browser.
+ *
+ * Unknown flags throw rather than being ignored: a mistyped `--tracks` on a tool
+ * whose whole job is to produce a plausible-looking image would otherwise be
+ * reported by nothing at all.
+ */
+export declare function parseArgs(argv: string[]): ParsedArgs;

package/esm/args.js

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+const NUMERIC = new Set(['width', 'height', 'scale', 'timeout', 'settle']);
+const FLAGS = new Set([
+    'fullPage',
+    'headed',
+    'verbose',
+    'help',
+    'allowUnsettled',
+]);
+const REPEATABLE = new Set(['track']);
+const STRINGS = new Set([
+    'hub',
+    'config',
+    'assembly',
+    'loc',
+    'session',
+    'sessionName',
+    'instance',
+    'out',
+]);
+// `--fullPage`, not `--full-page`: the flags match the option names in the
+// library API one for one, so a script and a command line say the same thing.
+// Aliases are the two abbreviations that are hard not to type.
+const ALIASES = { o: 'out', h: 'help' };
+function known(name) {
+    return (NUMERIC.has(name) ||
+        FLAGS.has(name) ||
+        REPEATABLE.has(name) ||
+        STRINGS.has(name));
+}
+/**
+ * Parse `jb2capture` flags. Split from the binary so the accepted shapes are
+ * unit-testable without launching a browser.
+ *
+ * Unknown flags throw rather than being ignored: a mistyped `--tracks` on a tool
+ * whose whole job is to produce a plausible-looking image would otherwise be
+ * reported by nothing at all.
+ */
+export function parseArgs(argv) {
+    const out = { tracks: [] };
+    for (const flag of FLAGS) {
+        out[flag] = false;
+    }
+    for (let i = 0; i < argv.length; i++) {
+        const arg = argv[i];
+        if (!arg.startsWith('-')) {
+            throw new Error(`unexpected argument "${arg}"`);
+        }
+        const bare = arg.replace(/^--?/, '');
+        const eq = bare.indexOf('=');
+        const rawName = eq === -1 ? bare : bare.slice(0, eq);
+        const name = ALIASES[rawName] ?? rawName;
+        if (!known(name)) {
+            throw new Error(`unknown flag "${arg}"`);
+        }
+        if (FLAGS.has(name)) {
+            out[name] = true;
+            continue;
+        }
+        const value = eq === -1 ? argv[++i] : bare.slice(eq + 1);
+        if (value === undefined) {
+            throw new Error(`--${name} needs a value`);
+        }
+        if (REPEATABLE.has(name)) {
+            ;
+            out.tracks.push(value);
+        }
+        else if (NUMERIC.has(name)) {
+            const n = Number(value);
+            if (!Number.isFinite(n)) {
+                throw new Error(`--${name} needs a number, got "${value}"`);
+            }
+            out[name] = n;
+        }
+        else {
+            out[name] = value;
+        }
+    }
+    return out;
+}

package/esm/bin.d.ts

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+#!/usr/bin/env node
+export {};

package/esm/bin.js

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+#!/usr/bin/env node
+import { readFileSync } from 'node:fs';
+import { parseArgs } from './args.js';
+import { captureJBrowse } from './capture.js';
+import { listHubTracks } from './hub.js';
+import { PAINT_CONTRACT_NOTE } from './sessionGate.js';
+import { jbrowseUrl } from './url.js';
+const HELP = `jb2capture — screenshot a live JBrowse 2 view, once it has finished drawing
+
+USAGE
+  jb2capture [flags] --out <file.png>    open a view, wait for it, screenshot it
+  jb2capture url [flags]                 print the URL instead of launching a browser
+  jb2capture list <hub> [filter]         list a hosted assembly's trackIds
+
+WHAT TO SHOW
+  --hub <name>          a genomes.jbrowse.org assembly: a UCSC db name (hg38, mm39)
+                        or a GenArk accession (GCA_.../GCF_...)
+  --config <url>        a config.json URL, for data that is not hosted there
+  --assembly <name>     assembly to open (defaults to --hub)
+  --loc <locstring>     where to go: chr1:1,000-2,000, or several space-separated
+                        for a discontinuous view. On a config with a text index —
+                        every UCSC assembly on genomes.jbrowse.org has one — a
+                        gene name such as BRCA1 also works.
+  --track <trackId>     a track to open; repeat for several
+  --session <json|path> a full session spec, for several views or per-display
+                        settings. Replaces --assembly/--loc/--track.
+  --instance <url>      JBrowse Web deployment to drive
+                        (default https://jbrowse.org/code/jb2/latest/)
+  --sessionName <name>  name the opened session carries
+
+THE IMAGE
+  --out, -o <file>      PNG to write (required unless using a subcommand)
+  --width <px>          viewport width (default 1400)
+  --height <px>         viewport height (default 900)
+  --scale <n>           device pixel ratio (default 2)
+  --fullPage            capture the whole scrollable page, not just the viewport
+
+WAITING
+  --timeout <ms>        budget per wait stage (default 60000)
+  --settle <ms>         extra pause after everything reports drawn (default 0)
+  --allowUnsettled      write the image anyway when a stage times out
+
+  Every stage is waited on for you: the session holding the assembly and tracks
+  you asked for, the view resolving, tracks fetching, displays painting, and any
+  leftover "Loading…" text. A stage that times out FAILS the run rather than
+  quietly handing back a half-drawn frame — raise --timeout, or pass
+  --allowUnsettled if you want the frame as it stands.
+
+OTHER
+  --headed              run with a visible browser window
+  --verbose             print browser console output (GPU noise filtered)
+  --help, -h            this text
+
+EXAMPLES
+  ## RefSeq genes and ClinVar at a gene, from hosted data, no setup
+  jb2capture --hub hg38 --loc BRCA1 \\
+    --track hg38-ncbiRefSeqCurated --track hg38-clinvarMain -o brca1.png
+
+  ## find the trackIds first
+  jb2capture list hg38 conservation
+
+  ## your own config, two loci side by side
+  jb2capture --config https://example.org/config.json --assembly mydata \\
+    --loc "chr3:25,325,000-25,361,000 chr10:58,716,500-58,718,500" -o two.png
+`;
+function readSession(value) {
+    const text = value.trimStart().startsWith('{')
+        ? value
+        : readFileSync(value, 'utf8');
+    const parsed = JSON.parse(text);
+    if (typeof parsed !== 'object' || parsed === null) {
+        throw new Error('--session must be a JSON object');
+    }
+    return parsed;
+}
+function urlOptions(args) {
+    return {
+        hub: args.hub,
+        config: args.config,
+        assembly: args.assembly,
+        loc: args.loc,
+        tracks: args.tracks.length ? args.tracks : undefined,
+        session: args.session ? readSession(args.session) : undefined,
+        sessionName: args.sessionName,
+        instance: args.instance,
+    };
+}
+async function runList(rest) {
+    const [hub, filter] = rest;
+    if (!hub) {
+        throw new Error('list needs an assembly, e.g. `jb2capture list hg38`. ' +
+            'Browse them at https://genomes.jbrowse.org.');
+    }
+    const tracks = await listHubTracks(hub, filter);
+    if (!tracks.length) {
+        throw new Error(filter
+            ? `no track in ${hub} matches "${filter}"`
+            : `${hub} publishes no tracks`);
+    }
+    const pad = Math.min(60, Math.max(...tracks.map(t => t.trackId.length)));
+    for (const t of tracks) {
+        console.log(`  ${t.trackId.padEnd(pad)}  ${(t.type ?? '').padEnd(18)}  ${t.name ?? ''}`);
+    }
+}
+async function main() {
+    const argv = process.argv.slice(2);
+    const [first, ...rest] = argv;
+    if (first === 'list') {
+        await runList(rest);
+        return;
+    }
+    const isUrlOnly = first === 'url';
+    const args = parseArgs(isUrlOnly ? rest : argv);
+    if (args.help || argv.length === 0) {
+        console.log(HELP);
+        return;
+    }
+    if (isUrlOnly) {
+        console.log(jbrowseUrl(urlOptions(args)));
+        return;
+    }
+    if (!args.out) {
+        throw new Error('--out <file.png> is required (or use `jb2capture url`)');
+    }
+    const { url, pending, paintContract, unsettled } = await captureJBrowse({
+        ...urlOptions(args),
+        out: args.out,
+        width: args.width,
+        height: args.height,
+        deviceScaleFactor: args.scale,
+        fullPage: args.fullPage,
+        headless: !args.headed,
+        timeout: args.timeout,
+        settleMs: args.settle,
+        allowUnsettled: args.allowUnsettled,
+        onConsole: args.verbose
+            ? text => {
+                console.error(`  [page] ${text}`);
+            }
+            : undefined,
+    });
+    console.log(`wrote ${args.out}`);
+    console.log(`from  ${url}`);
+    // Reached only when the wait either succeeded or was explicitly overridden, so
+    // these are notes on an image that exists rather than failures. They still get
+    // said out loud: "everything painted", "we stopped waiting" and "paint could
+    // not be measured here" all look identical in a PNG.
+    if (unsettled.length) {
+        console.error(`warning: --allowUnsettled: ${unsettled.join('; ')}`);
+    }
+    if (pending.length) {
+        console.error(`warning: ${pending.length} display(s) had not finished drawing at capture time ` +
+            `(${pending.join(', ')}). Raise --timeout, or --settle for a slow remote file.`);
+    }
+    else if (!paintContract) {
+        console.error(`note: ${PAINT_CONTRACT_NOTE}`);
+    }
+}
+try {
+    await main();
+}
+catch (error) {
+    console.error(`jb2capture: ${error instanceof Error ? error.message : error}`);
+    process.exitCode = 1;
+}

package/esm/browser.d.ts

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+export declare const SANDBOX_CHROME_ARGS: string[];
+export declare const BASE_CHROME_ARGS: string[];
+export declare function findChromeExecutable(): string | undefined;
+export declare function isBrowserConsoleNoise(text: string): boolean;

package/esm/browser.js

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+import fs from 'node:fs';
+// Just the sandbox flags, for the scripts that MEASURE cross-origin behaviour
+// (COOP/COEP isolation, cancelled cross-origin fetches) and would be measuring
+// nothing with web security off. They used to spell this
+// `BASE_CHROME_ARGS.filter(a => a !== '--disable-web-security')`, which silently
+// stops subtracting the day another security flag is added below.
+export const SANDBOX_CHROME_ARGS = ['--no-sandbox', '--disable-setuid-sandbox'];
+// Chrome flags both harnesses launch with. Backend-specific flags
+// (--disable-gpu, --enable-unsafe-swiftshader, --disable-popup-blocking) are
+// appended by each caller.
+export const BASE_CHROME_ARGS = [
+    ...SANDBOX_CHROME_ARGS,
+    '--disable-web-security',
+];
+const CHROME_PATHS = [
+    '/usr/bin/google-chrome',
+    '/usr/bin/chromium-browser',
+    '/usr/bin/chromium',
+];
+// First installed system Chrome/Chromium, or undefined to let Puppeteer use its
+// bundled browser. `CHROME_PATH` wins, so a run can be pinned to one binary --
+// which is how you answer "did the browser move under us?" when a figure regen
+// reports the whole corpus as changed.
+//
+// Measured 2026-08-02, because that question came up and the answer was no: the
+// same spec rendered under Chrome 147.0.7727.57 and 151.0.7922.47 produces
+// byte-identical PNGs, and the system package's 151.0.7922.47 -> .71 roll
+// likewise changed nothing. So a corpus-wide diff is accumulated app change
+// since the last `Bump snaps` sweep, not the browser -- don't chase it here.
+export function findChromeExecutable() {
+    return process.env.CHROME_PATH ?? CHROME_PATHS.find(p => fs.existsSync(p));
+}
+// GPU/WebGL lifecycle chatter that isn't a real error. Real GPU failures
+// (`context LOST`, `GL error`) are deliberately NOT suppressed.
+const NOISE_NEEDLES = [
+    'favicon',
+    'GPU stall',
+    '[GPU] WebGPU not supported',
+    '[GPU] No compatible GPU adapter',
+    '[GPU] WebGPU initialization failed',
+    '[GPU] WebGL2 unavailable',
+    '[GPU] WebGPU device creation failed',
+    'GroupMarkerNotSet',
+    'Automatic fallback to software WebGL',
+    'No available adapters',
+    'Failed to create WebGPU Context Provider',
+];
+export function isBrowserConsoleNoise(text) {
+    if (text.includes('[WebGL2Hal #')) {
+        return !text.includes('context LOST') && !text.includes('GL error');
+    }
+    return NOISE_NEEDLES.some(n => text.includes(n));
+}