brukerconverter - npm Package Compare versions

Comparing version 6.0.9 to 6.0.10-pre.1678714014

lib/index.js

@@ -29,4 +29,4 @@ 'use strict';
   } = options;
-
   const experiments = {};
+  const fileList = fileCollection.files.map((file) => file.relativePath);
   for (let file of fileCollection) {
@@ -38,2 +38,3 @@ let procno;
     let id;
+    // console.log(file.name);
     const parts = file.relativePath.split('/');
@@ -47,3 +48,3 @@ if (file.relativePath.match(/\/pdata\/\d+\//)) {
       id = parts.slice(0, -3).join('/');
-    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+    } else if (isRawOrAcquisitionFile(file, fileList)) {
       const firstLevel = parts.indexOf(file.name);
@@ -107,2 +108,6 @@ expno = Number(parts[firstLevel - 1]);
     }
+
+    if (file.name === 'QuantFactorSample.xml') {
+      experiment.quantFactorSample = file;
+    }
   }
@@ -196,2 +201,10 @@ if (processingNumbers) {
 
+function isRawOrAcquisitionFile(file, fileList) {
+  return (
+    file.name.match(/^(ser|acqus|acqu2s|QuantFactorSample.xml)$/) ||
+    (file.name.match(/^(fid)$/) &&
+      fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
+  );
+}
+
 function joinInfoMeta(target, toAppend) {
@@ -384,2 +397,4 @@ for (let key in toAppend.meta) {
 
+  if (files.quantFactorSample) addEreticFactor(result, files);
+
   if (files['1r'] || files['1i']) {
@@ -400,2 +415,11 @@ await setProcessedSpectrumData(
 
+async function addEreticFactor(result, files) {
+  const quantFactorSample = (await files.quantFactorSample.text()).match(
+    /<Application[\w\W]+<Eretic_Factor>(?<ereticFactor>[\d.]+)/,
+  );
+  if (quantFactorSample) {
+    result.info.ereticFactor = Number(quantFactorSample.groups.ereticFactor);
+  }
+}
+
 function mergeMetadata(main, complement) {
@@ -402,0 +426,0 @@ for (let key in complement.meta) {

package.json

 {
   "name": "brukerconverter",
-  "version": "6.0.9",
+  "version": "6.0.10-pre.1678714014",
   "description": "Parse and convert Bruker raw data",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/__tests__/convertFileList.test.js

@@ -15,2 +15,13 @@ import { join } from 'path';
     const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'ereticMethod'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+    });
+
+    expect(results[0].info).toHaveProperty('ereticFactor');
+    expect(results[0].info.ereticFactor).toBeCloseTo(2441.11043387, 4);
+  });
+  it('convert folder without expno level', async () => {
+    const fileCollection = await fileCollectionFromPath(
       join(__dirname, 'data/withoutExpno'),
@@ -38,2 +49,39 @@ );
   });
+  it('keep only fid', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+      filter: { dataSelection: 'fid' },
+    });
+
+    expect(results).toHaveLength(1);
+    expect(results[0].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      is1D: true,
+      isFID: true,
+    });
+    expect(results[0].spectra[0].data.re).toHaveLength(65536 / 2);
+  });
+  it('keep only ft', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/withoutExpno'),
+    );
+    const results = await convertFileCollection(fileCollection, {
+      converter: { keepFiles: true },
+      filter: { dataSelection: 'ft' },
+    });
+
+    expect(results).toHaveLength(1);
+    expect(results[0].source).toMatchCloseTo({
+      name: 'withoutExpno',
+      expno: 0,
+      procno: 1,
+      is1D: true,
+      isFT: true,
+    });
+    expect(results[0].spectra[0].data.re).toHaveLength(65536 / 2);
+  });
   it('advanced example', async () => {
@@ -40,0 +88,0 @@ const fileCollection = await getCoffee();

src/__tests__/groupByExperiments.test.js

@@ -68,2 +68,24 @@ import { join } from 'path';
   });
+  it('keep only ft', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'ft',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0].procno).toBe(1);
+  });
+  it('keep only FID', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/10'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'fid',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(10);
+    expect(results[0]).not.toHaveProperty('procno');
+  });
 });
@@ -70,0 +92,0 @@ describe('groupByExperiments', () => {

src/groupByExperiments.js

@@ -21,4 +21,4 @@ /**
   } = options;
-
   const experiments = {};
+  const fileList = fileCollection.files.map((file) => file.relativePath);
   for (let file of fileCollection) {
@@ -30,2 +30,3 @@ let procno;
     let id;
+    // console.log(file.name);
     const parts = file.relativePath.split('/');
@@ -39,3 +40,3 @@ if (file.relativePath.match(/\/pdata\/\d+\//)) {
       id = parts.slice(0, -3).join('/');
-    } else if (file.name.match(/^(ser|fid|acqus|acqu2s)$/)) {
+    } else if (isRawOrAcquisitionFile(file, fileList)) {
       const firstLevel = parts.indexOf(file.name);
@@ -99,2 +100,6 @@ expno = Number(parts[firstLevel - 1]);
     }
+
+    if (file.name === 'QuantFactorSample.xml') {
+      experiment.quantFactorSample = file;
+    }
   }
@@ -187,1 +192,9 @@ if (processingNumbers) {
 }
+
+function isRawOrAcquisitionFile(file, fileList) {
+  return (
+    file.name.match(/^(ser|acqus|acqu2s|QuantFactorSample.xml)$/) ||
+    (file.name.match(/^(fid)$/) &&
+      fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
+  );
+}

src/util/convert1D.js

@@ -11,2 +11,4 @@ import { joinInfoMeta } from './joinMetaInfo.js';
 
+  if (files.quantFactorSample) addEreticFactor(result, files);
+
   if (files['1r'] || files['1i']) {
@@ -26,1 +28,10 @@ await setProcessedSpectrumData(
 }
+
+async function addEreticFactor(result, files) {
+  const quantFactorSample = (await files.quantFactorSample.text()).match(
+    /<Application[\w\W]+<Eretic_Factor>(?<ereticFactor>[\d.]+)/,
+  );
+  if (quantFactorSample) {
+    result.info.ereticFactor = Number(quantFactorSample.groups.ereticFactor);
+  }
+}

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Found 1 instance in 1 package

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Contains native code (e.g., compiled binaries or shared libraries). Including native code can obscure malicious behavior.

Found 1 instance in 1 package

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

Fixed alerts

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Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

1438136

increased by24.88%

Number of package files

41

increased by10.81%

Lines of code

1750

increased by6.64%

Worsened metrics

Number of low quality alerts

2

increased by100%

Number of medium supply chain risk alerts

7

increased by16.67%

No dependency changes