34 update to use filecollection

package.json

@@ -42,27 +42,27 @@
   },
   "devDependencies": {
     "babel-cli": "^6.26.0",
-    "babel-jest": "^28.1.3",
+    "babel-jest": "^29.1.2",
     "babel-plugin-remove-comments": "^2.0.0",
     "babel-plugin-transform-es2015-modules-commonjs": "^6.26.2",
     "babel-preset-babili": "^0.1.4",
     "cheminfo-tools": "^1.23.3",
     "codecov": "^3.8.2",
-    "eslint": "^8.22.0",
+    "eslint": "^8.24.0",
     "eslint-config-cheminfo": "^8.0.2",
     "esm": "^3.2.25",
-    "jest": "^28.1.3",
-    "nmredata-data-test": "^0.3.0",
+    "jest": "^29.1.2",
+    "nmredata-data-test": "0.4.0",
     "prettier": "^2.7.1",
-    "rollup": "^2.78.0"
+    "rollup": "^2.79.1"
   },
   "dependencies": {
-    "filelist-utils": "^0.7.1",
+    "filelist-utils": "^0.11.0",
     "jszip": "^3.10.1",
-    "openchemlib": "^8.0.0",
+    "openchemlib": "^8.0.1",
     "openchemlib-utils": "^2.0.0"
   },
   "volta": {
     "node": "16.16.0"
   }
-}
+}

src/NmrRecord.js

@@ -10,19 +10,20 @@ export class NmrRecord {
     if (!(nmrRecord instanceof Object)) {
       throw new Error('Cannot be called directly');
     }
-    let { sdfData, files } = nmrRecord;
-    this.files = files;
+    let { sdfData, fileCollection } = nmrRecord;
+    this.fileCollection = fileCollection;
     this.sdfData = sdfData;
     this.activeElement = 0;
     this.nbSamples = sdfData.length;
   }
 
-  static async fromFileList(files) {
+  static async fromFileCollection(fileCollection) {
+    const files = fileCollection.files;
     if (!Array.isArray(files) || files.length < 1) {
       throw new Error('should be at least 1 file');
     }
-    const sdfData = await getSDF(files);
-    return new NmrRecord({ sdfData, files });
+    const sdfData = await getSDF(fileCollection);
+    return new NmrRecord({ sdfData, fileCollection });
   }
 
   getMol(i = this.activeElement) {
@@ -72,7 +73,7 @@ export class NmrRecord {
   toJSON(i = this.activeElement) {
     let index = this.checkIndex(i);
     return nmrRecordToJSON({
-      files: this.files,
+      fileCollection: this.fileCollection,
       sdf: this.sdfData[index],
     });
   }
@@ -115,7 +116,7 @@ export class NmrRecord {
  */
 // there is an error here, we should be able to export any index in sdf, add options use activeElement.
 export const nmrRecordToJSON = (options = {}) => {
-  let { sdf, molecule, files } = options;
+  let { sdf, molecule, fileCollection } = options;
   let sdfFile = checkSdf(sdf);
   molecule = !molecule
     ? OCLMolecule.fromMolfile(sdfFile.molecules[0].molfile)
@@ -128,7 +129,7 @@ export const nmrRecordToJSON = (options = {}) => {
   return nmredataToJSON(nmredata, {
     molecule,
     root: sdfFile.root,
-    files,
+    fileCollection,
   });
 };
 

src/converter/__tests__/nmredataToJSON.test.js

@@ -17,7 +17,7 @@ describe('NMReData to nmrium', () => {
     expect(experiment).toBe('zg30');
 
     expect(
-      source.file.files.map((file) => file.webkitRelativePath),
+      source.file.fileCollection.files.map((file) => file.relativePath),
     ).toStrictEqual([
       'AN-menthol/10/uxnmr.par',
       'AN-menthol/10/prosol_History',

src/converter/util/toJSON/getBrukerFiles.js

@@ -1,5 +1,7 @@
+import { FileCollection } from 'filelist-utils';
+
 export async function getBrukerFiles(tag, options) {
-  let { files, root } = options;
+  let { fileCollection, root } = options;
 
   let locationLine = tag.data.find((e) => e.value.spectrum_location);
 
@@ -14,17 +16,16 @@ export async function getBrukerFiles(tag, options) {
   let toCheck2 = pathSpectrum.replace(/.*\/[0-9]+\/pdata\/([0-9]+)\/.*/, '$1');
 
   let brukerFolder = [];
-  for (let file of files) {
+  for (let file of fileCollection) {
     if (
-      toCheck !==
-      file.webkitRelativePath.replace(/([.*/]*\w+\/[0-9]+\/).*/, '$1')
+      toCheck !== file.relativePath.replace(/([.*/]*\w+\/[0-9]+\/).*/, '$1')
     ) {
       continue;
     }
-    if (file.webkitRelativePath.match('pdata')) {
+    if (file.relativePath.match('pdata')) {
       if (
         toCheck2 !==
-        file.webkitRelativePath.replace(/.*\/[0-9]+\/pdata\/([0-9]+)\/.*/, '$1')
+        file.relativePath.replace(/.*\/[0-9]+\/pdata\/([0-9]+)\/.*/, '$1')
       ) {
         continue;
       }
@@ -34,6 +35,6 @@ export async function getBrukerFiles(tag, options) {
   return {
     name: `${pathSpectrum}`,
     type: 'brukerFiles',
-    files: brukerFolder,
+    fileCollection: new FileCollection(brukerFolder),
   };
 }

src/converter/util/toJSON/getJcamp.js

@@ -1,5 +1,7 @@
+import { FileCollection } from 'filelist-utils';
+
 export async function getJcamp(tag, options) {
-  let { files, root } = options;
+  let { fileCollection, root } = options;
   let locationLine = tag.data.find((e) => e.value.jcamp_location);
 
   if (!locationLine) {
@@ -9,14 +11,16 @@ export async function getJcamp(tag, options) {
 
   let relativePath = locationLine.value.jcamp_location;
   let pathJcamp = root + relativePath.replace(/file:/s, '');
-  const jcampFile = files.find((file) => file.webkitRelativePath === pathJcamp);
+  const jcampFile = fileCollection.files.find(
+    (file) => file.relativePath === pathJcamp,
+  );
   if (!jcampFile) {
     new Error(`There is not jcamp with path: ${pathJcamp}`);
     return;
   }
   return {
     name: pathJcamp,
     type: 'jcamp',
-    files: [jcampFile],
+    fileCollection: new FileCollection([jcampFile]),
   };
 }

src/reader/readNmrRecord.js

@@ -1,4 +1,4 @@
-import { fileListFromZip } from 'filelist-utils';
+import { fileCollectionFromZip } from 'filelist-utils';
 
 import { NmrRecord } from '../NmrRecord';
 
@@ -8,6 +8,6 @@ import { NmrRecord } from '../NmrRecord';
  * @return {} An Object with two properties zip and sdfFiles.
  */
 export async function readNmrRecord(zipFile) {
-  const files = await fileListFromZip(zipFile);
-  return NmrRecord.fromFileList(files);
+  const fileCollection = await fileCollectionFromZip(zipFile);
+  return NmrRecord.fromFileCollection(fileCollection);
 }

src/util/getSDF.js

@@ -8,7 +8,7 @@ import { parseSDF } from '../parser/parseSDF';
 export async function getSDF(files) {
   let result = [];
   for (const file of files) {
-    const pathFile = file.webkitRelativePath.split('/');
+    const pathFile = file.relativePath.split('/');
     if (/^[^.].+sdf$/.exec(file.name)) {
       const filename = file.name.replace(/\.sdf/, '');
       const root = pathFile.slice(0, pathFile.length - 1).join('/');