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Merged
NishaSharma14 merged 2 commits into from
Feb 23, 2026
Merged

refactor(nmr-cli): capture errors using fiflogger #106

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e84b049
chore(nmr-cli): update dependencies
hamed-musallam Feb 19, 2026
05580df
refactor(nmr-cli): capture errors using fiflogger
hamed-musallam Feb 23, 2026
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3 changes: 2 additions & 1 deletion app/scripts/nmr-cli/package-lock.json
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3 changes: 2 additions & 1 deletion app/scripts/nmr-cli/package.json
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
"@zakodium/nmrium-core": "^0.6.5",
"@zakodium/nmrium-core-plugins": "^0.6.39",
"axios": "^1.13.5",
"fifo-logger": "^2.0.1",
"file-collection": "^6.6.0",
"json-stream-stringify": "^3.1.6",
"lodash.merge": "^4.6.2",
Expand All @@ -36,4 +37,4 @@
"ts-node": "^10.9.2",
"typescript": "^5.9.3"
}
}
}
74 changes: 48 additions & 26 deletions app/scripts/nmr-cli/src/parse/prase-spectra.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -13,19 +13,25 @@ import { Filters1DManager, Filters2DManager } from 'nmr-processing'
import yargs from 'yargs'
import { createWriteStream } from 'fs'
import { JsonStreamStringify } from 'json-stream-stringify';
import { FifoLogger } from 'fifo-logger'

type RequiredKey<T, K extends keyof T> = Omit<T, K> & Required<Pick<T, K>>;

function toMessage(e: unknown): string {
return e instanceof Error ? e.message : String(e)
}


const parsingOptions: ParsingOptions = {
onLoadProcessing: { autoProcessing: true },
selector: { general: { dataSelection: 'preferFT' } },
experimentalFeatures: true,
};


interface Snapshot {
id: string;
image: string | null;
error: string | null;
}

const core = init()
Expand All @@ -41,7 +47,7 @@ async function launchBrowser() {
return playwright.firefox.launch();
}

async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>): Promise<Snapshot[]> {
async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>, logger: FifoLogger): Promise<Snapshot[]> {
const { data: { spectra } = { spectra: [] }, version } = nmriumState;

if (!spectra?.length) return [];
Expand Down Expand Up @@ -77,15 +83,10 @@ async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>): Pr
await page.locator('text=Loading').waitFor({ state: 'hidden' });

const snapshot = await page.locator('#nmrSVG .container').screenshot();
snapshots.push({ id: spectrum.id, image: snapshot.toString('base64'), error: null });
snapshots.push({ id: spectrum.id, image: snapshot.toString('base64') });

} catch (e) {
snapshots.push({
id: spectrum.id,
image: null,
error: e instanceof Error ? e.message : String(e),
});

logger.error({ id: spectrum.id, stage: 'snapshot', details: toMessage(e) }, 'Failed to capture snapshot for spectrum with id: ' + spectrum.id);
// browser crashed — close and recreate for next spectrum
await browser.close().catch(() => { });
browser = await launchBrowser();
Expand All @@ -104,23 +105,41 @@ interface ProcessSpectraOptions {
autoDetection: boolean; autoProcessing: boolean;
}

function processSpectra(data: NmriumData, options: ProcessSpectraOptions) {
function processSpectra(data: NmriumData, options: ProcessSpectraOptions, logger: FifoLogger) {

const { autoDetection = false, autoProcessing = false } = options

for (let index = 0; index < data.spectra.length; index++) {
const inputSpectrum = data.spectra[index]
const is2D = isSpectrum2D(inputSpectrum);
const spectrum = is2D ? initiateDatum2D(inputSpectrum) : initiateDatum1D(inputSpectrum);
let spectrum = null;
try {

spectrum = is2D ? initiateDatum2D(inputSpectrum) : initiateDatum1D(inputSpectrum);
} catch (e) {
logger.error({ id: inputSpectrum.id, stage: 'parsing', details: toMessage(e) }, 'Failed to parse spectrum with id: ' + inputSpectrum.id);
continue;
}

if (autoProcessing) {
isSpectrum2D(spectrum) ? Filters2DManager.reapplyFilters(spectrum) : Filters1DManager.reapplyFilters(spectrum)
try {

isSpectrum2D(spectrum) ? Filters2DManager.reapplyFilters(spectrum) : Filters1DManager.reapplyFilters(spectrum)
} catch (e) {
logger.error({ id: inputSpectrum.id, stage: 'processing', details: toMessage(e) }, 'Failed to process spectrum with id: ' + inputSpectrum.id);
}
}

if (autoDetection && spectrum.info.isFt) {
isSpectrum2D(spectrum) ? detectZones(spectrum) : detectRanges(spectrum);
try {
isSpectrum2D(spectrum) ? detectZones(spectrum) : detectRanges(spectrum);
} catch (e) {
logger.error({ id: inputSpectrum.id, stage: 'detection', details: toMessage(e) }, 'Failed to detect spectrum peaks with id: ' + inputSpectrum.id);
}
}

if (!spectrum) continue;

data.spectra[index] = spectrum;
}

Expand All @@ -143,16 +162,17 @@ function outputResult(result: any, outputPath?: string) {

async function processAndSerialize(
nmriumState: Partial<NmriumState>,
options: FileOptionsArgs
options: FileOptionsArgs,
logger: FifoLogger
) {
const { s: enableSnapshot = false, p: autoProcessing = false, d: autoDetection = false, o, r } = options;

if (nmriumState.data) {
processSpectra(nmriumState.data, { autoDetection, autoProcessing });
processSpectra(nmriumState.data, { autoDetection, autoProcessing }, logger);
}

const images: Snapshot[] = enableSnapshot
? await captureSpectraViewAsBase64(nmriumState)
? await captureSpectraViewAsBase64(nmriumState, logger)
: [];

const { data, version } = core.serializeNmriumState(
Expand All @@ -169,11 +189,11 @@ async function processAndSerialize(
spectra[i] = { ...spectra[i], info, meta }
}
}

outputResult({ data, version, images }, o);
const errors = logger.getLogs({ minLevel: 'error' })
outputResult({ data, version, images, errors }, o);
}

async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>) {
async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>, logger: FifoLogger) {
const { u: url } = options;

const { pathname: relativePath, origin: baseURL } = new URL(url)
Expand All @@ -186,13 +206,14 @@ async function loadSpectrumFromURL(options: RequiredKey<FileOptionsArgs, 'u'>) {
baseURL,
}

const [nmriumState] = await core.readFromWebSource(source, parsingOptions);

processAndSerialize(nmriumState, options)
const [nmriumState] = await core.readFromWebSource(source, { ...parsingOptions, logger });

processAndSerialize(nmriumState, options, logger)

}

async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'dir'>) {
async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'dir'>, logger: FifoLogger) {
const { dir: path } = options;

const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
Expand All @@ -203,25 +224,26 @@ async function loadSpectrumFromFilePath(options: RequiredKey<FileOptionsArgs, 'd

const {
nmriumState
} = await core.read(fileCollection, parsingOptions)
} = await core.read(fileCollection, { ...parsingOptions, logger })

processAndSerialize(nmriumState, options)
processAndSerialize(nmriumState, options, logger)

}


function parseSpectra(argv: yargs.ArgumentsCamelCase<FileOptionsArgs>
) {
const logger = new FifoLogger();

const { u, dir } = argv;
// Handle parsing the spectra file logic based on argv options
if (u) {
loadSpectrumFromURL({ u, ...argv });
loadSpectrumFromURL({ u, ...argv }, logger);
}


if (dir) {
loadSpectrumFromFilePath({ dir, ...argv });
loadSpectrumFromFilePath({ dir, ...argv }, logger);
}


Expand Down