brukerconverter - npm Package Compare versions

Comparing version 4.1.6 to 4.1.7-pre.1664466065

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;
+  fileList: FileCollection;
   expno: number;
@@ -72,3 +74,3 @@ is2D?: boolean;
   expno: number;
-  fileList: PartialFileList;
+  fileList: FileCollection;
   processedData?: ProcessedData;
@@ -80,3 +82,6 @@ is2D?: boolean;
 
-export function groupByExperiments(fileList: PartialFileList, options?: GroupByExperimentsOptions): Experiment[];
+export function groupByExperiments(
+  fileList: FileCollection,
+  options?: GroupByExperimentsOptions,
+): Experiment[];
 
@@ -89,4 +94,4 @@ export interface ConverterOptions {
 export interface ConvertFileListOptions {
-  filter?: GroupByExperimentsOptions,
-  converter?: ConverterOptions,
+  filter?: GroupByExperimentsOptions;
+  converter?: ConverterOptions;
 }
@@ -109,3 +114,3 @@
   yUnit: string;
-  isXYdata: boolean,
+  isXYdata: boolean;
   observeFrequency: number;
@@ -117,3 +122,3 @@ deltaX: number;
 export interface Spectrum2D extends Spectrum1D {
-  pageValue: number
+  pageValue: number;
 }
@@ -134,3 +139,3 @@
     isFID: boolean;
-  }
+  };
 }
@@ -161,8 +166,10 @@
     isFID: boolean;
-  }
+  };
 }
 
-
 type SpectraData = SpectraData1D | SpectraData2D;
 
-export async function convertFileList(fileList: PartialFileList, options?: ConvertFileListOptions): Promise<SpectraData[]>
+export function convertFileList(
+  fileList: FileCollection,
+  options?: ConvertFileListOptions,
+): Promise<SpectraData[]>;

lib/index.js

@@ -5,2 +5,3 @@ 'use strict';
 
+var filelistUtils = require('filelist-utils');
 var jcampconverter = require('jcampconverter');
@@ -47,4 +48,4 @@ var iobuffer = require('iobuffer');
     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]);
@@ -54,3 +55,3 @@ 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]);
@@ -137,3 +138,2 @@ name = parts[parts.length - 3] || parts[parts.length - 2];
   }
-  // console.log('experiments', experiments)
   // We convert the object to an array
@@ -191,3 +191,3 @@ // and before filtering we will move all the processedData
   }
-  // console.log(experimentsArray)
+
   return experimentsArray;
@@ -609,3 +609,9 @@ }
 
+function convertZip(zip, options) {
+  const fileList = filelistUtils.fileCollectionFromZip(zip);
+  return convertFileList(fileList, options);
+}
+
 exports.convertFileList = convertFileList;
+exports.convertZip = convertZip;
 exports.groupByExperiments = groupByExperiments;

package.json

 {
   "name": "brukerconverter",
-  "version": "4.1.6",
+  "version": "4.1.7-pre.1664466065",
   "description": "Parse and convert Bruker raw data",
@@ -36,3 +36,3 @@ "main": "lib/index.js",
     "@types/jest": "^28.1.6",
-    "bruker-data-test": "0.2.1",
+    "bruker-data-test": "0.3.0-pre.1664462893",
     "cheminfo-build": "^1.1.11",
@@ -48,3 +48,3 @@ "eslint": "^8.20.0",
     "cheminfo-types": "^1.4.0",
-    "filelist-utils": "^0.5.0",
+    "filelist-utils": "^0.11.0",
     "iobuffer": "^5.1.0",
@@ -55,2 +55,2 @@ "is-any-array": "^2.0.0",
   }
-}
+}

src/__tests__/convertFileList.test.js

@@ -11,3 +11,3 @@ import { getCoffee } from 'bruker-data-test';
   it('advanced example', async () => {
-    const fileList = getCoffee();
+    const fileList = await getCoffee();
     const results = await convertFileList(fileList);
@@ -14,0 +14,0 @@ expect(results).toHaveLength(18);

src/__tests__/convertZip.test.js

@@ -1,3 +0,3 @@
-import { getZipped } from 'bruker-data-test';
-import { fileListFromZip } from 'filelist-utils';
+import { getData } from 'bruker-data-test';
+import { fileCollectionFromZip } from 'filelist-utils';
 
@@ -8,6 +8,4 @@ import { convertFileList } from '../convertFileList.js';
   it('cyclospirin proton spectrum', async () => {
-    const zip = await getZipped()
-      .filter((file) => file.name === 'cyclosporin_1h.zip')[0]
-      .arrayBuffer();
-    const fileList = await fileListFromZip(zip);
+    const zip = await getData('cyclosporin_1h.zip');
+    const fileList = await fileCollectionFromZip(zip);
     let result = await convertFileList(fileList, {
@@ -24,6 +22,4 @@ xy: true,
   it('cyclosporin hmbc', async () => {
-    const zip = await getZipped()
-      .filter((file) => file.name === 'cyclosporin_hmbc.zip')[0]
-      .arrayBuffer();
-    const fileList = await fileListFromZip(zip);
+    const zip = await getData('cyclosporin_hmbc.zip');
+    const fileList = await fileCollectionFromZip(zip);
     let result = await convertFileList(fileList, {
@@ -30,0 +26,0 @@ converter: {

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

@@ -37,4 +37,4 @@ /**
     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

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

New alerts

No v1

Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

50095

1.45%

Number of package files

21

5%

Lines of code

1431

1.56%

Worsened metrics

Number of low quality alerts

2

100%

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