brukerconverter - npm Package Compare versions

Comparing version 6.0.10 to 6.1.0

lib/index.js

@@ -29,3 +29,2 @@ 'use strict';
   } = options;
-
   const experiments = {};
@@ -106,2 +105,6 @@ const fileList = fileCollection.files.map((file) => file.relativePath);
     }
+
+    if (file.name === 'QuantFactorSample.xml') {
+      experiment.quantFactorSample = file;
+    }
   }
@@ -140,9 +143,4 @@ if (processingNumbers) {
 
-    const processedKeys = Object.keys(processed);
-    const hasRawData = experiment.ser || experiment.fid;
-
-    if (
-      (hasRawData && dataSelection !== 'ft' && dataSelection !== 'preferFT') ||
-      (dataSelection === 'preferFT' && !processedKeys.length)
-    ) {
+    if (shouldAddRawData(experiments[key], dataSelection)) {
+      const processedKeys = Object.keys(processed);
       if (processedKeys.length > 0) {
@@ -162,2 +160,3 @@ const firstProcessed = processed[processedKeys[0]];
 
+    const hasRawData = 'ser' in experiment || 'fid' in experiment;
     if (
@@ -199,3 +198,3 @@ dataSelection === 'fid' ||
   return (
-    file.name.match(/^(ser|acqus|acqu2s)$/) ||
+    file.name.match(/^(ser|acqus|acqu2s|QuantFactorSample.xml)$/) ||
     (file.name.match(/^(fid)$/) &&
@@ -206,2 +205,18 @@ fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
 
+function shouldAddRawData(experiment, dataSelection) {
+  const { processedData: processed } = experiment;
+  const processedKeys = Object.keys(processed);
+  const hasProcessData =
+    processedKeys.length > 0 &&
+    ('1r' in processed[processedKeys[0]] ||
+      '1i' in processed[processedKeys[0]]);
+
+  const hasRawData = 'ser' in experiment || 'fid' in experiment;
+  const notPreferFt = dataSelection !== 'ft' && dataSelection !== 'preferFT';
+  const preferFtWithoutProcessedData =
+    dataSelection === 'preferFT' && !hasProcessData;
+
+  return hasRawData && (notPreferFt || preferFtWithoutProcessedData);
+}
+
 function joinInfoMeta(target, toAppend) {
@@ -394,2 +409,4 @@ for (let key in toAppend.meta) {
 
+  if (files.quantFactorSample) addEreticFactor(result, files);
+
   if (files['1r'] || files['1i']) {
@@ -410,2 +427,11 @@ 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) {
@@ -412,0 +438,0 @@ for (let key in complement.meta) {

package.json

 {
   "name": "brukerconverter",
-  "version": "6.0.10",
+  "version": "6.1.0",
   "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'),
@@ -17,0 +28,0 @@ );

src/__tests__/groupByExperiments.test.js

@@ -44,2 +44,13 @@ import { join } from 'path';
   });
+  it('priorize FT without processed data', async () => {
+    const fileCollection = await fileCollectionFromPath(
+      join(__dirname, 'data/11'),
+    );
+    const results = groupByExperiments(fileCollection, {
+      dataSelection: 'preferFT',
+    });
+    expect(results).toHaveLength(1);
+    expect(results[0].expno).toBe(11);
+    expect(results[0]).toHaveProperty('fid');
+  });
   it('priorize FID', async () => {
@@ -46,0 +57,0 @@ const fileCollection = await fileCollectionFromPath(

src/groupByExperiments.js

@@ -21,3 +21,2 @@ /**
   } = options;
-
   const experiments = {};
@@ -98,2 +97,6 @@ const fileList = fileCollection.files.map((file) => file.relativePath);
     }
+
+    if (file.name === 'QuantFactorSample.xml') {
+      experiment.quantFactorSample = file;
+    }
   }
@@ -132,9 +135,4 @@ if (processingNumbers) {
 
-    const processedKeys = Object.keys(processed);
-    const hasRawData = experiment.ser || experiment.fid;
-
-    if (
-      (hasRawData && dataSelection !== 'ft' && dataSelection !== 'preferFT') ||
-      (dataSelection === 'preferFT' && !processedKeys.length)
-    ) {
+    if (shouldAddRawData(experiments[key], dataSelection)) {
+      const processedKeys = Object.keys(processed);
       if (processedKeys.length > 0) {
@@ -154,2 +152,3 @@ const firstProcessed = processed[processedKeys[0]];
 
+    const hasRawData = 'ser' in experiment || 'fid' in experiment;
     if (
@@ -191,3 +190,3 @@ dataSelection === 'fid' ||
   return (
-    file.name.match(/^(ser|acqus|acqu2s)$/) ||
+    file.name.match(/^(ser|acqus|acqu2s|QuantFactorSample.xml)$/) ||
     (file.name.match(/^(fid)$/) &&
@@ -197,1 +196,17 @@ fileList.includes(file.relativePath.replace(/fid$/, 'acqus')))
 }
+
+function shouldAddRawData(experiment, dataSelection) {
+  const { processedData: processed } = experiment;
+  const processedKeys = Object.keys(processed);
+  const hasProcessData =
+    processedKeys.length > 0 &&
+    ('1r' in processed[processedKeys[0]] ||
+      '1i' in processed[processedKeys[0]]);
+
+  const hasRawData = 'ser' in experiment || 'fid' in experiment;
+  const notPreferFt = dataSelection !== 'ft' && dataSelection !== 'preferFT';
+  const preferFtWithoutProcessedData =
+    dataSelection === 'preferFT' && !hasProcessData;
+
+  return hasRawData && (notPreferFt || preferFtWithoutProcessedData);
+}

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

Native code

Supply chain risk

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

Found 2 instances in 1 package

Fixed alerts

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Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

1724544

increased by49.44%

Number of package files

46

increased by24.32%

Lines of code

1779

increased by3.79%

Worsened metrics

Number of medium supply chain risk alerts

8

increased by33.33%

No dependency changes