feat: migrate to nmrium-core and nmrium-core-plugins

app/scripts/nmr-cli/Dockerfile

@@ -1,7 +1,7 @@
 # build the image ` docker build --tag nmr-cli  . ` 
 # run the container ` docker run -it nmr-cli bash `
 
-FROM mcr.microsoft.com/playwright:v1.53.0-jammy
+FROM mcr.microsoft.com/playwright:v1.54.1-jammy
 
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]

app/scripts/nmr-cli/package.json

@@ -15,15 +15,16 @@
     "nmr-cli": "./build/index.js"
   },
   "dependencies": {
+    "@zakodium/nmrium-core": "^0.1.3",
+    "@zakodium/nmrium-core-plugins": "^0.1.4",
     "axios": "^1.10.0",
     "filelist-utils": "^1.11.3",
-    "nmr-load-save": "^3.6.0",
     "nmr-processing": "^19.0.0",
-    "playwright": "^1.53.0",
+    "playwright": "^1.54.1",
     "yargs": "^18.0.0"
   },
   "devDependencies": {
-    "@types/node": "^24.0.3",
+    "@types/node": "^24.0.14",
     "@types/yargs": "^17.0.33",
     "ts-node": "^10.9.2",
     "typescript": "^5.8.3"

app/scripts/nmr-cli/src/index.ts

@@ -3,7 +3,7 @@ import yargs, { type Argv, type CommandModule, type Options } from 'yargs'
 import { loadSpectrumFromURL, loadSpectrumFromFilePath } from './prase-spectra'
 import { generateSpectrumFromPublicationString } from './publication-string'
 import { parsePredictionCommand } from './prediction/parsePredictionCommand'
-import { hideBin } from 'yargs/helpers';
+import { hideBin } from 'yargs/helpers'
 
 const usageMessage = `
 Usage: nmr-cli  <command> [options]
@@ -126,4 +126,4 @@ yargs(hideBin(process.argv))
   .command(parsePredictionCommand)
   .showHelpOnFail(true)
   .help()
-  .parse()
+  .parse()

app/scripts/nmr-cli/src/prase-spectra.ts

@@ -1,129 +1,130 @@
-import { join, isAbsolute } from "path";
-import { type NmriumState, read } from "nmr-load-save";
-import { fileCollectionFromWebSource, fileCollectionFromPath } from "filelist-utils";
-import playwright from 'playwright';
-
+import { join, isAbsolute } from 'path'
+import { type NmriumState } from '@zakodium/nmrium-core'
+import init from '@zakodium/nmrium-core-plugins'
+import {
+  fileCollectionFromWebSource,
+  fileCollectionFromPath,
+} from 'filelist-utils'
+import playwright from 'playwright'
 
 interface Snapshot {
-    image: string,
-    id: string;
+  image: string
+  id: string
 }
 
+const core = init()
 
 function generateNMRiumURL() {
-    const baseURL = process.env['BASE_NMRIUM_URL'] || '';
-    const url = new URL(baseURL)
-    url.searchParams.append('workspace', "embedded")
-    return url.toString()
+  const baseURL = process.env['BASE_NMRIUM_URL'] || ''
+  const url = new URL(baseURL)
+  url.searchParams.append('workspace', 'embedded')
+  return url.toString()
 }
 
-
 async function captureSpectraViewAsBase64(nmriumState: Partial<NmriumState>) {
-    const { data: { spectra } = { spectra: [] }, version } = nmriumState;
-    const browser = await playwright.chromium.launch()
-    const context = await browser.newContext(playwright.devices['Desktop Chrome HiDPI'])
-    const page = await context.newPage()
-
-    const url = generateNMRiumURL()
-
-    await page.goto(url)
+  const { data: { spectra } = { spectra: [] }, version } = nmriumState
+  const browser = await playwright.chromium.launch()
+  const context = await browser.newContext(
+    playwright.devices['Desktop Chrome HiDPI']
+  )
+  const page = await context.newPage()
 
-    await page.locator('text=Loading').waitFor({ state: 'hidden' });
+  const url = generateNMRiumURL()
 
-    let snapshots: Snapshot[] = []
+  await page.goto(url)
 
-    for (const spectrum of spectra || []) {
-        const spectrumObject = {
-            version,
-            data: {
-                spectra: [{ ...spectrum }],
-            }
+  await page.locator('text=Loading').waitFor({ state: 'hidden' })
 
-        }
+  let snapshots: Snapshot[] = []
 
-        // convert typed array to array
-        const stringObject = JSON.stringify(spectrumObject, (key, value: unknown) => {
-            return ArrayBuffer.isView(value) ? Array.from(value as unknown as Iterable<unknown>) : value
-        })
+  for (const spectrum of spectra || []) {
+    const spectrumObject = {
+      version,
+      data: {
+        spectra: [{ ...spectrum }],
+      },
+    }
 
-        // load the spectrum into NMRium using the custom event
-        await page.evaluate(
-            `
+    // convert typed array to array
+    const stringObject = JSON.stringify(
+      spectrumObject,
+      (key, value: unknown) => {
+        return ArrayBuffer.isView(value)
+          ? Array.from(value as unknown as Iterable<unknown>)
+          : value
+      }
+    )
+
+    // load the spectrum into NMRium using the custom event
+    await page.evaluate(
+      `
         window.postMessage({ type: "nmr-wrapper:load", data:{data: ${stringObject},type:"nmrium"}}, '*');
         `
-        )
-
-        //wait for NMRium process and load spectra
-        await page.locator('text=Loading').waitFor({ state: 'hidden' });
-
-        // take a snapshot for the spectrum
-        try {
-            const snapshot = await page.locator('#nmrSVG .container').screenshot()
-
-            snapshots.push({
-                image: snapshot.toString('base64'),
-                id: spectrum.id,
-            })
-        } catch (e) {
-            console.log(e)
-        }
-    }
+    )
 
-    await context.close()
-    await browser.close()
+    //wait for NMRium process and load spectra
+    await page.locator('text=Loading').waitFor({ state: 'hidden' })
 
-    return snapshots;
-}
+    // take a snapshot for the spectrum
+    try {
+      const snapshot = await page.locator('#nmrSVG .container').screenshot()
 
-async function loadSpectrumFromURL(url: string, enableSnapshot = false) {
-    const { pathname: relativePath, origin: baseURL } = new URL(url);
-    const source = {
-        entries: [
-            {
-                relativePath,
-            }
-        ],
-        baseURL
-    };
-    const fileCollection = await fileCollectionFromWebSource(source, {});
-
-    const {
-        nmriumState: { data, version },
-    } = await read(fileCollection);
-
-    let images: Snapshot[] = []
-
-    if (enableSnapshot) {
-        images = await captureSpectraViewAsBase64({ data, version });
+      snapshots.push({
+        image: snapshot.toString('base64'),
+        id: spectrum.id,
+      })
+    } catch (e) {
+      console.log(e)
     }
+  }
 
+  await context.close()
+  await browser.close()
 
-    return { data, version, images };
+  return snapshots
 }
 
+async function loadSpectrumFromURL(url: string, enableSnapshot = false) {
+  const { pathname: relativePath, origin: baseURL } = new URL(url)
+  const source = {
+    entries: [
+      {
+        relativePath,
+      },
+    ],
+    baseURL,
+  }
+  const fileCollection = await fileCollectionFromWebSource(source, {})
+
+  const {
+    nmriumState: { data, version },
+  } = await core.read(fileCollection)
+
+  let images: Snapshot[] = []
+
+  if (enableSnapshot) {
+    images = await captureSpectraViewAsBase64({ data, version })
+  }
+
+  return { data, version, images }
+}
 
 async function loadSpectrumFromFilePath(path: string, enableSnapshot = false) {
-    const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
+  const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
 
-    const fileCollection = await fileCollectionFromPath(dirPath, {});
+  const fileCollection = await fileCollectionFromPath(dirPath, {})
 
-    const {
-        nmriumState: { data, version }
-    } = await read(fileCollection);
+  const {
+    nmriumState: { data, version },
+  } = await core.read(fileCollection)
 
-    let images: Snapshot[] = []
+  let images: Snapshot[] = []
 
-    if (enableSnapshot) {
-        images = await captureSpectraViewAsBase64({ data, version });
-    }
+  if (enableSnapshot) {
+    images = await captureSpectraViewAsBase64({ data, version })
+  }
 
-
-    return { data, version, images };
+  return { data, version, images }
 }
 
-
-export {
-    loadSpectrumFromFilePath,
-    loadSpectrumFromURL
-};
-
+export { loadSpectrumFromFilePath, loadSpectrumFromURL }