brukerconverter - npm Package Compare versions

Comparing version 4.1.7 to 5.0.0

src/convertFileCollection.js

+import { groupByExperiments } from './groupByExperiments';
+import { convertOneExperiment } from './util/convertOneExperiment.js';
+
+/**
+ *
+ * @param {*} fileCollection
+ * @param {object} [options={}]
+ * @param {object} [options.filter]
+ * @param {object} [options.converter]
+ * @returns
+ */
+export async function convertFileCollection(fileCollection, options = {}) {
+  const { filter, converter } = options;
+  const results = [];
+  const experiments = groupByExperiments(fileCollection, filter);
+  for (let experiment of experiments) {
+    const result = await convertOneExperiment(experiment, converter);
+    if (result) {
+      results.push(result);
+    }
+  }
+  return results;
+}

src/helpers/convertZip.js

+import { fileCollectionFromZip } from 'filelist-utils';
+
+import { convertFileCollection } from '../convertFileCollection';
+
+export function convertZip(zip, options) {
+  const fileCollection = fileCollectionFromZip(zip);
+  return convertFileCollection(fileCollection, options);
+}

brukerconverter.d.ts

 import { DoubleArray } from 'cheminfo-types';
-import type { PartialFile, PartialFileList } from 'filelist-utils';
+import type { FileCollectionItem, FileCollection } from 'filelist-utils';
 import { DoubleMatrix } from 'ml-spectra-processing';
@@ -16,3 +16,5 @@
 
-type FirstLevelPartialFile = Partial<Record<FirstLevelKeys, PartialFile>>;
+type FirstLevelPartialFile = Partial<
+  Record<FirstLevelKeys, FileCollectionItem>
+>;
 
@@ -59,3 +61,3 @@ export interface GroupByExperimentsOptions {
   name: string;
-  fileList: PartialFileList;
+  fileCollection: FileCollection;
   expno: number;
@@ -72,3 +74,3 @@ is2D?: boolean;
   expno: number;
-  fileList: PartialFileList;
+  fileCollection: FileCollection;
   processedData?: ProcessedData;
@@ -81,3 +83,3 @@ is2D?: boolean;
 export function groupByExperiments(
-  fileList: PartialFileList,
+  fileCollection: FileCollection,
   options?: GroupByExperimentsOptions,
@@ -166,4 +168,4 @@ ): Experiment[];
 export function convertFileList(
-  fileList: PartialFileList,
+  fileCollection: FileCollection,
   options?: ConvertFileListOptions,
 ): Promise<SpectraData[]>;

lib/index.js

@@ -5,2 +5,3 @@ 'use strict';
 
+var filelistUtils = require('filelist-utils');
 var jcampconverter = require('jcampconverter');
@@ -13,3 +14,3 @@ var iobuffer = require('iobuffer');
  * Retrieve the list of files for further process
- * @param {File[]} fileList
+ * @param {FileCollection[]} fileList
  * @param {object} [options={}]
@@ -48,4 +49,4 @@ * @param {number|number[]} [options.processingNumber] - processing number to select, default the smallest number
     let id;
-    const parts = file.webkitRelativePath.split('/');
-    if (file.webkitRelativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
+    const parts = file.relativePath.split('/');
+    if (file.relativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
       currentProcessingNo = Number(parts[parts.length - 2]);
@@ -55,3 +56,3 @@ currentExperimentNo = Number(parts[parts.length - 4]);
       id = parts.slice(0, -3).join('/');
-    } else if (file.webkitRelativePath.match(/[0-9]+\/.*$/)) {
+    } else if (file.relativePath.match(/[0-9]+\/.*$/)) {
       currentExperimentNo = Number(parts[parts.length - 2]);
@@ -138,3 +139,2 @@ name = parts[parts.length - 3] || parts[parts.length - 2];
   }
-  // console.log('experiments', experiments)
   // We convert the object to an array
@@ -192,3 +192,3 @@ // and before filtering we will move all the processedData
   }
-  // console.log(experimentsArray)
+
   return experimentsArray;
@@ -591,3 +591,3 @@ }
  *
- * @param {*} fileList
+ * @param {*} fileCollection
  * @param {object} [options={}]
@@ -598,6 +598,6 @@ * @param {object} [options.filter]
  */
-async function convertFileList(fileList, options = {}) {
+async function convertFileCollection(fileCollection, options = {}) {
   const { filter, converter } = options;
   const results = [];
-  const experiments = groupByExperiments(fileList, filter);
+  const experiments = groupByExperiments(fileCollection, filter);
   for (let experiment of experiments) {
@@ -612,3 +612,9 @@ const result = await convertOneExperiment(experiment, converter);
 
-exports.convertFileList = convertFileList;
+function convertZip(zip, options) {
+  const fileCollection = filelistUtils.fileCollectionFromZip(zip);
+  return convertFileCollection(fileCollection, options);
+}
+
+exports.convertFileCollection = convertFileCollection;
+exports.convertZip = convertZip;
 exports.groupByExperiments = groupByExperiments;

package.json

 {
   "name": "brukerconverter",
-  "version": "4.1.7",
+  "version": "5.0.0",
   "description": "Parse and convert Bruker raw data",
@@ -35,20 +35,20 @@ "main": "lib/index.js",
     "@babel/plugin-transform-modules-commonjs": "^7.18.6",
-    "@types/jest": "^28.1.6",
-    "bruker-data-test": "0.2.1",
+    "@types/jest": "^29.1.1",
+    "bruker-data-test": "0.4.0",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.20.0",
+    "eslint": "^8.24.0",
     "eslint-config-cheminfo": "^8.0.2",
-    "jest": "^28.1.3",
+    "jest": "^29.1.2",
     "jest-matcher-deep-close-to": "^3.0.2",
     "prettier": "^2.7.1",
-    "rollup": "^2.77.2"
+    "rollup": "^2.79.1"
   },
   "dependencies": {
     "cheminfo-types": "^1.4.0",
-    "filelist-utils": "^0.5.0",
+    "filelist-utils": "^0.11.0",
     "iobuffer": "^5.1.0",
     "is-any-array": "^2.0.0",
     "jcampconverter": "^9.0.2",
-    "ml-spectra-processing": "^11.9.0"
+    "ml-spectra-processing": "^11.12.0"
   }
-}
+}

README.md

@@ -21,8 +21,8 @@ #brukerconverter
 const { convertFileList } = require('brukerconverter');
-const { fileListFromZip } = require('fileList-utils');
+const { fileListFromZip } = require('fileCollection-utils');
 const { getZipped } = require('bruker-data-test');
 
 async function asyncCall(zip) {
-  const fileList = await fileListFromZip(zip);
-  const result = await convertFileList(fileList);
+  const fileCollection = await fileListFromZip(zip);
+  const result = await convertFileList(fileCollection);
   console.log(result);
@@ -44,4 +44,4 @@ //...{ spectra, meta, source }
 async function asyncCall(path) {
-  const fileList = await fileListFromPath(path);
-  const result = await convertFileList(fileList);
+  const fileCollection = await fileListFromPath(path);
+  const result = await convertFileList(fileCollection);
   console.log(result);
@@ -48,0 +48,0 @@ //...{ spectra, meta, source }

src/__tests__/convertFileList.test.js

 import { getCoffee } from 'bruker-data-test';
 import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 
-import { convertFileList } from '../convertFileList.js';
+import { convertFileCollection } from '../convertFileCollection.js';
 
@@ -9,6 +9,6 @@ expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
 jest.setTimeout(60000);
-describe('convertFileList', () => {
+describe('convertFileCollection', () => {
   it('advanced example', async () => {
-    const fileList = getCoffee();
-    const results = await convertFileList(fileList);
+    const fileCollection = await getCoffee();
+    const results = await convertFileCollection(fileCollection);
     expect(results).toHaveLength(18);
@@ -15,0 +15,0 @@

src/__tests__/convertZip.test.js

@@ -1,13 +0,11 @@
-import { getZipped } from 'bruker-data-test';
-import { fileListFromZip } from 'filelist-utils';
+import { getData } from 'bruker-data-test';
+import { fileCollectionFromZip } from 'filelist-utils';
 
-import { convertFileList } from '../convertFileList.js';
+import { convertFileCollection } from '../convertFileCollection.js';
 
 describe('Test with zip file', () => {
   it('cyclospirin proton spectrum', async () => {
-    const zip = await getZipped()
-      .filter((file) => file.name === 'cyclosporin_1h.zip')[0]
-      .arrayBuffer();
-    const fileList = await fileListFromZip(zip);
-    let result = await convertFileList(fileList, {
+    const zip = await getData('cyclosporin_1h.zip');
+    const fileCollection = await fileCollectionFromZip(zip);
+    let result = await convertFileCollection(fileCollection, {
       xy: true,
@@ -23,7 +21,5 @@ keepSpectra: true,
   it('cyclosporin hmbc', async () => {
-    const zip = await getZipped()
-      .filter((file) => file.name === 'cyclosporin_hmbc.zip')[0]
-      .arrayBuffer();
-    const fileList = await fileListFromZip(zip);
-    let result = await convertFileList(fileList, {
+    const zip = await getData('cyclosporin_hmbc.zip');
+    const fileCollection = await fileCollectionFromZip(zip);
+    let result = await convertFileCollection(fileCollection, {
       converter: {
@@ -30,0 +26,0 @@ xy: true,

src/__tests__/groupByExperiments.test.js

@@ -6,9 +6,10 @@ import { getCoffee } from 'bruker-data-test';
 describe('groupByExperiments', () => {
-  const fileList = getCoffee();
   it('no options', async () => {
-    const results = groupByExperiments(fileList);
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection);
     expect(results).toHaveLength(18);
   });
   it('ignore fid and 2d', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       ignore2D: true,
@@ -28,3 +29,4 @@ ignoreFID: true,
   it('ignore ft and 2d', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       ignore2D: true,
@@ -44,3 +46,4 @@ ignoreFT: true,
   it('ignore fid and 1d', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       ignore1D: true,
@@ -52,3 +55,4 @@ ignoreFID: true,
   it('ignore ft and 1d', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       ignore1D: true,
@@ -60,3 +64,4 @@ ignoreFT: true,
   it('get only procNo equal 1', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       processingNumber: 1,
@@ -67,3 +72,4 @@ });
   it('get only the first procno ignoring raw data', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       onlyFirstProcessedData: false,
@@ -75,3 +81,4 @@ ignoreFID: true,
   it('get only the second procno ignoring raw data', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       processingNumber: 2,
@@ -83,3 +90,4 @@ ignoreFID: true,
   it('get only procNo equal 1 ignoring raw data', async () => {
-    const results = groupByExperiments(fileList, {
+    const fileCollection = await getCoffee();
+    const results = groupByExperiments(fileCollection, {
       processingNumber: 1,
@@ -86,0 +94,0 @@ ignoreFID: true,

src/groupByExperiments.js

 /**
  * Retrieve the list of files for further process
- * @param {File[]} fileList
+ * @param {FileCollection[]} fileList
  * @param {object} [options={}]
@@ -37,4 +37,4 @@ * @param {number|number[]} [options.processingNumber] - processing number to select, default the smallest number
     let id;
-    const parts = file.webkitRelativePath.split('/');
-    if (file.webkitRelativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
+    const parts = file.relativePath.split('/');
+    if (file.relativePath.match(/\/pdata\/[0-9]+\/.*$/)) {
       currentProcessingNo = Number(parts[parts.length - 2]);
@@ -44,3 +44,3 @@ currentExperimentNo = Number(parts[parts.length - 4]);
       id = parts.slice(0, -3).join('/');
-    } else if (file.webkitRelativePath.match(/[0-9]+\/.*$/)) {
+    } else if (file.relativePath.match(/[0-9]+\/.*$/)) {
       currentExperimentNo = Number(parts[parts.length - 2]);
@@ -127,3 +127,2 @@ name = parts[parts.length - 3] || parts[parts.length - 2];
   }
-  // console.log('experiments', experiments)
   // We convert the object to an array
@@ -181,4 +180,4 @@ // and before filtering we will move all the processedData
   }
-  // console.log(experimentsArray)
+
   return experimentsArray;
 }

src/index.js

@@ -1,2 +0,3 @@
-export { convertFileList } from './convertFileList';
+export { convertZip } from './helpers/convertZip';
+export { convertFileCollection } from './convertFileCollection';
 export { groupByExperiments } from './groupByExperiments';

src/convertFileList.js

-import { groupByExperiments } from './groupByExperiments';
-import { convertOneExperiment } from './util/convertOneExperiment.js';
-
-/**
- *
- * @param {*} fileList
- * @param {object} [options={}]
- * @param {object} [options.filter]
- * @param {object} [options.converter]
- * @returns
- */
-export async function convertFileList(fileList, options = {}) {
-  const { filter, converter } = options;
-  const results = [];
-  const experiments = groupByExperiments(fileList, filter);
-  for (let experiment of experiments) {
-    const result = await convertOneExperiment(experiment, converter);
-    if (result) {
-      results.push(result);
-    }
-  }
-  return results;
-}

No alert changes

Improved metrics

Total package byte prevSize

50344

1.93%

Number of package files

21

5%

Lines of code

1431

1.06%

Dependency changes

• + Added

  cross-fetch@3.2.0
  (transitive)

• + Added

  filelist-utils@0.11.0
  (transitive)

• + Added

  node-fetch@2.7.0
  (transitive)

• + Added

  tr46@0.0.3
  (transitive)

• + Added

  webidl-conversions@3.0.1
  (transitive)

• + Added

  whatwg-url@5.0.0
  (transitive)

• - Removed

  filelist-utils@0.5.0
  (transitive)

• Updated

  filelist-utils@^0.11.0

• Updated

  ml-spectra-processing@^11.12.0