refactor: parallelize parse spectra pipeline across concurrent worker…

app/scripts/nmr-cli/Dockerfile

@@ -32,6 +32,9 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+# Downgrade to Node 22 for nmr-processing compatibility
+RUN npm install -g n && n 22 && hash -r
+
 COPY package.json ./
 
 RUN npm install
@@ -40,9 +43,11 @@ COPY . ./
 
 RUN npm run build
 
+# Install nmr-cli as a global package
+RUN npm install -g .
 
-# Install the nmr-cli as a global package 
+# Usage examples (run after `docker run -it nmr-cli bash`):
+#   nmr-cli parse-spectra -u https://s3.uni-jena.de/nmrxiv/production/archive/1368b8fd-3af7-48f7-8b6d-13de9c1ecf8b/492-62-6.zip -s
 # For example, nmr-cli parse-spectra -u https://s3.uni-jena.de/nmrxiv/production/archive/d5ec45db-d984-46e9-bb72-c43fd4a463fa/Sali_Eth.zip -s
 # For example, nmr-cli parse-spectra -u https://cheminfo.github.io/bruker-data-test/data/zipped/aspirin-1h.zip
 # nmr-cli predict -n "1H" --id 1 --type "nmr;1H;1d" --shifts "1" --solvent "Dimethylsulphoxide-D6 (DMSO-D6, C2D6SO)" -m $"\n Ketcher  6122516162D 1   1.00000     0.00000     0\n\n 16 17  0  0  0  0  0  0  0  0999 V2000\n    1.1954   -4.6484    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -4.6479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0622   -4.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.9258   -5.6488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    1.1954   -5.6533    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    2.0644   -6.1483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7902   -4.1495    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6574   -4.6498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    3.7964   -6.1512    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0\n    4.6596   -5.6458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5228   -4.1488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5277   -6.1421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    6.3895   -4.6477    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    5.5216   -3.1488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0\n    7.2548   -4.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n    8.1215   -4.6455    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0\n  3  1  2  0  0  0  0\n  1  5  1  0  0  0  0\n  5  6  2  0  0  0  0\n  6  4  1  0  0  0  0\n  4  2  1  0  0  0  0\n  2  3  1  0  0  0  0\n  4  9  1  0  0  0  0\n  9 10  2  0  0  0  0\n 10  8  1  0  0  0  0\n  8  7  2  0  0  0  0\n  7  2  1  0  0  0  0\n  8 11  1  0  0  0  0\n 10 12  1  0  0  0  0\n 11 13  1  0  0  0  0\n 11 14  2  0  0  0  0\n 13 15  1  0  0  0  0\n 15 16  1  0  0  0  0\nM  END"
-RUN npm install . -g

app/scripts/nmr-cli/package.json

@@ -32,7 +32,7 @@
   },
   "devDependencies": {
     "@types/lodash.merge": "^4.6.9",
-    "@types/node": "^26.2.0",
+    "@types/node": "^26.4.0",
     "@types/yargs": "^17.0.35",
     "ts-node": "^10.9.2",
     "typescript": "^5.9.3"

app/scripts/nmr-cli/src/parse/browser-manager.ts

@@ -0,0 +1,163 @@
+import playwright from 'playwright';
+import type { FifoLogger } from 'fifo-logger';
+import type { SpectrumWorker } from './spectrum-worker';
+import { Spectrum } from '@zakodium/nmr-types';
+import { Snapshot } from './spectrum-snapshot';
+import { toMessage } from './utility/toMessage';
+
+// How long to wait for the NMRium "Loading" indicator to appear/disappear
+// before giving up on a single spectrum's snapshot. Prevents one stuck page
+// from hanging the entire pipeline.
+export const SNAPSHOT_LOADING_TIMEOUT_MS = 30_000;
+
+// A single flaky failure (a slow spectrum tipping over the loading timeout,
+// a one-off page hiccup) shouldn't permanently cost a spectrum its snapshot,
+// so each capture gets one retry on a fresh page before giving up.
+export const SNAPSHOT_MAX_ATTEMPTS = 2;
+
+// Owns the single shared Firefox process. Multiple lanes each get their own
+// context/page from it. `reset` is guarded so that if several lanes hit a
+// dead browser at once, only the first one actually relaunches — the rest
+// just see `current` has already changed and pick up the fresh instance.
+export class BrowserManager {
+    private current: Promise<playwright.Browser> | null = null;
+
+    async get(): Promise<playwright.Browser> {
+        if (!this.current) {
+            this.current = playwright.firefox.launch();
+        }
+        return this.current;
+    }
+
+    async reset(stale: playwright.Browser): Promise<void> {
+        if (this.current && (await this.current) === stale) {
+            const toClose = this.current;
+            this.current = null;
+            await (await toClose).close().catch(() => { });
+        }
+    }
+
+    async closeAll(): Promise<void> {
+        if (this.current) {
+            const toClose = this.current;
+            this.current = null;
+            await (await toClose).close().catch(() => { });
+        }
+    }
+}
+
+// One snapshot lane = one browser tab, reused across every spectrum it's
+// assigned. Launching the browser/context happens once per lane; every
+// spectrum after the first gets a `page.reload()` (not a new context or
+// browser) before its `nmr-wrapper:load` message, so each snapshot starts
+// from a genuinely empty NMRium instance instead of relying on `load`
+// merging vs. replacing the previous spectrum's state. A reload of an
+// already-booted SPA is far cheaper than relaunching the browser/context,
+// so this keeps the speed win while removing the state-leak risk.
+export class SnapshotLane {
+    private context: playwright.BrowserContext | null = null;
+    private page: playwright.Page | null = null;
+    private hasLoadedSpectrum = false;
+
+    constructor(private manager: BrowserManager, private url: string) { }
+
+    private async ensurePage(): Promise<playwright.Page> {
+        if (this.page && !this.page.isClosed()) {
+            if (this.hasLoadedSpectrum) {
+                await this.page.reload();
+                await this.page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
+            }
+            return this.page;
+        }
+        const browser = await this.manager.get();
+        this.context = await browser.newContext(playwright.devices['Desktop Chrome HiDPI']);
+        this.page = await this.context.newPage();
+        await this.page.goto(this.url);
+        await this.page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
+        this.hasLoadedSpectrum = false;
+        return this.page;
+    }
+
+    // Discards this lane's page/context so the next attempt (or the next
+    // spectrum, if we're giving up) starts from a clean page instead of
+    // whatever broken state caused the failure. Only escalates to a full
+    // browser relaunch if the browser process itself is gone.
+    private async recover(): Promise<void> {
+        await this.context?.close().catch(() => { });
+        this.context = null;
+        this.page = null;
+        this.hasLoadedSpectrum = false;
+
+        const browser = await this.manager.get();
+        if (!browser.isConnected()) {
+            await this.manager.reset(browser);
+        }
+    }
+
+    private async attemptCapture(
+        spectrum: Spectrum,
+        version: unknown,
+        spectrumWorker: SpectrumWorker
+    ): Promise<string> {
+        const page = await this.ensurePage();
+
+        const stringObject = await spectrumWorker.run('serialize', spectrum, version);
+
+        // Passed as a Playwright function argument rather than spliced into an
+        // evaluated script string, so a backtick or `${...}` sequence anywhere
+        // in the spectrum data can't break (or hijack) the script.
+        await page.evaluate(
+            ({ data }) => {
+                window.postMessage({ type: 'nmr-wrapper:load', data: { data, type: 'nmrium' } }, '*');
+            },
+            { data: JSON.parse(stringObject) }
+        );
+
+        await page.locator('text=Loading').waitFor({ state: 'hidden', timeout: SNAPSHOT_LOADING_TIMEOUT_MS });
+
+        const snapshot = await page.locator('#nmrSVG .container').screenshot();
+        this.hasLoadedSpectrum = true;
+        return snapshot.toString('base64');
+    }
+
+    async capture(
+        spectrum: Spectrum,
+        id: string,
+        version: unknown,
+        spectrumWorker: SpectrumWorker,
+        logger: FifoLogger
+    ): Promise<Snapshot> {
+        let lastError: unknown;
+
+        for (let attempt = 1; attempt <= SNAPSHOT_MAX_ATTEMPTS; attempt++) {
+            const start = Date.now();
+            try {
+                const image = await this.attemptCapture(spectrum, version, spectrumWorker);
+                logger.info(
+                    { id, stage: 'snapshot', attempt, durationMs: Date.now() - start },
+                    `Captured snapshot for spectrum: ${id}`
+                );
+                return { id, image };
+            } catch (e) {
+                lastError = e;
+                logger.error(
+                    { id, stage: 'snapshot', attempt, durationMs: Date.now() - start, details: toMessage(e) },
+                    `Snapshot attempt ${attempt}/${SNAPSHOT_MAX_ATTEMPTS} failed for spectrum: ${id}`
+                );
+                await this.recover();
+            }
+        }
+
+        logger.error(
+            { id, stage: 'snapshot', details: toMessage(lastError) },
+            `Giving up on snapshot for spectrum: ${id} after ${SNAPSHOT_MAX_ATTEMPTS} attempts`
+        );
+        return { id, image: null };
+    }
+
+    async dispose(): Promise<void> {
+        await this.context?.close().catch(() => { });
+        this.context = null;
+        this.page = null;
+    }
+}