refactor: combine the functionality of nmr-snapshot-cli with nmr-cli …

…and remove nmr-snapshot-cli3

app/scripts/nmr-cli/Dockerfile

@@ -1,15 +1,19 @@
 # build the image ` docker build --tag nmr-cli  . ` 
 # run the container ` docker run -it nmr-cli bash `
 
-FROM node:20.9.0-alpine
-# a temporary command to add bash to the Docker image to be able to run the container with an interactive Shell for testing purpose
-RUN apk update && apk add bash
+FROM mcr.microsoft.com/playwright:v1.40.0-jammy
+
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
 WORKDIR /app
 
+#ENV BASE_NMRIUM_URL=https://nmrium.nmrxiv.org/
+ENV BASE_NMRIUM_URL=https://nmriumdev.nmrxiv.org/
+
+
 COPY package.json ./
 COPY package-lock.json ./
+
 RUN npm install
 
 COPY . ./

app/scripts/nmr-cli/bin/index.js

@@ -1,64 +1,162 @@
 #!/usr/bin/env node
-const {join,isAbsolute}= require("path");
+const { join, isAbsolute } = require("path");
 const yargs = require("yargs");
 const loader = require("nmr-load-save");
 const fileUtils = require("filelist-utils");
+const playwright = require('playwright');
 
-const usageMessage ="Usage: nmr-cli -u <url> or -p <path>" 
+const usageMessage = "Usage: nmr-cli -u <url> or -p <path> -s<Optional parameter to capture spectra snapshots>"
+
+
+/**
+ * How to Use the Command Line Tool:
+ * Example 1: Process spectra files from a URL
+ * Usage: nmr-cli -u https://example.com/file.zip
+ * -------------------------------------------------------------------------
+ * Example 2: process a spectra files from a directory < nmr-cli  -p /path/to/directory >
+ * Usage: nmr-cli  -p /path/to/directory
+ * -------------------------------------------------------------------------
+ * you could also combine the above examples with an optional parameter to capturing a snapshot using the -s option
+ * 
+ */
 
 const options = yargs
- .usage(usageMessage)
- .option("u", { alias: "url", describe: "File URL", type: "string",nargs:1})
- .option("p", { alias: "path", describe: "Directory path", type: "string",nargs:1}).showHelpOnFail();
-
-  async function loadSpectrumFromURL(url) {
-    const {pathname:relativePath,origin:baseURL} = new URL(url);
-    const source = {
-        entries: [
-          {
-            relativePath,
-          }
-        ],
-        baseURL
-      };
-    const fileCollection = await fileUtils.fileCollectionFromWebSource(source,{});
-
-    const {
-      nmriumState: { data },
-    } = await loader.read(fileCollection);
-    return data;
+  .usage(usageMessage)
+  .option("u", { alias: "url", describe: "File URL", type: "string", nargs: 1 })
+  .option("p", { alias: "path", describe: "Directory path", type: "string", nargs: 1 })
+  .option("s", { alias: "capture-snapshot", describe: "Capture snapshot", type: "boolean" }).showHelpOnFail();
+
+
+
+
+function generateNMRiumURL() {
+  const baseURL = process.env['BASE_NMRIUM_URL'];
+  const url = new URL(baseURL)
+  url.searchParams.append('workspace', "embedded")
+  return url.toString()
+}
+
+async function captureSpectraViewAsBase64(nmriumState) {
+  const { data: { 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)
+
+  await page.locator('text=Loading').waitFor({ state: 'hidden' });
+
+  let snapshots = []
+
+  for (const spectrum of spectra || []) {
+    const spectrumObject = {
+      version,
+      data: {
+        spectra: [{ ...spectrum }],
+      }
+
+    }
+
+    // convert typed array to array
+    const stringObject = JSON.stringify(spectrumObject, (key, value) => {
+      return ArrayBuffer.isView(value) ? Array.from(value) : 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()
+
+  return snapshots;
+}
 
-  async function loadSpectrumFromFilePath(path) {
-    const dirPath = isAbsolute(path)?path:join(process.cwd(),path)
-
-    const fileCollection = await fileUtils.fileCollectionFromPath(dirPath,{});
-
-    const {
-      nmriumState: { data },
-    } = await loader.read(fileCollection);
-    return data;
+async function loadSpectrumFromURL(url, enableSnapshot = false) {
+  const { pathname: relativePath, origin: baseURL } = new URL(url);
+  const source = {
+    entries: [
+      {
+        relativePath,
+      }
+    ],
+    baseURL
+  };
+  const fileCollection = await fileUtils.fileCollectionFromWebSource(source, {});
+
+  const {
+    nmriumState: { data, version },
+  } = await loader.read(fileCollection);
+
+  let images = []
+
+  if (enableSnapshot) {
+    images = await captureSpectraViewAsBase64({ data, version });
   }
 
 
-  const parameters = options.argv;
+  return { data, version, images };
+}
+
+
+async function loadSpectrumFromFilePath(path, enableSnapshot = false) {
+  const dirPath = isAbsolute(path) ? path : join(process.cwd(), path)
+
+  const fileCollection = await fileUtils.fileCollectionFromPath(dirPath, {});
+
+  const {
+    nmriumState: { data, version }
+  } = await loader.read(fileCollection);
+
+  let images = []
 
-if(parameters.u && parameters.p){
+  if (enableSnapshot) {
+    images = await captureSpectraViewAsBase64({ data, version });
+  }
+
+
+  return { data, version, images };
+}
+
+
+const parameters = options.argv;
+
+if (parameters.u && parameters.p) {
   options.showHelp();
-}else{
+} else {
 
-  if(parameters.u){
-    loadSpectrumFromURL(parameters.u).then((result)=>{
-    console.log(JSON.stringify(result))
- })
+  if (parameters.u) {
+    loadSpectrumFromURL(parameters.u, parameters.s).then((result) => {
+      console.log(JSON.stringify(result))
+    })
 
   }
 
-  if(parameters.p){
-    loadSpectrumFromFilePath(parameters.p).then((result)=>{
+  if (parameters.p) {
+    loadSpectrumFromFilePath(parameters.p, parameters.s).then((result) => {
       console.log(JSON.stringify(result))
-   })
+    })
   }
 
 }

app/scripts/nmr-cli/package.json

@@ -14,7 +14,8 @@
   },
   "dependencies": {
     "filelist-utils": "^1.10.2",
-    "nmr-load-save": "^0.22.4",
-    "yargs": "^17.7.2"
+    "nmr-load-save": "^0.23.3",
+    "yargs": "^17.7.2",
+    "playwright": "^1.40.0"
   }
-}
+}