brukerconverter - npm Package Compare versions

Comparing version 6.1.4 to 6.1.5-pre.1691494258

lib/index.js

@@ -79,3 +79,3 @@ 'use strict';
       processedData.fileCollectionItems.push(file); // check if it can be moved into the conditional block
-      if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
+      if (file.name.match(/^(1r|1i|2rr|procs|proc2s|integrals.txt)$/)) {
         processedData[file.name] = file;
@@ -175,2 +175,3 @@ }
         experimentsArray.push({
+          integrals: oneProcessed['integrals.txt'],
           acqus: experiment.acqus,
@@ -190,3 +191,2 @@ acqu2s: experiment.acqu2s,
   }
-
   return experimentsArray;
@@ -217,2 +217,43 @@ }
 
+async function addIntegrals(result, files) {
+  const integralFile = files.integrals;
+  let text = await integralFile.text();
+  text = text.split(/\n/);
+  const info = text[1]
+    .replace(/^\s*/, '')
+    .replace(/(?<=\w)[\t]+/g, ';')
+    .replace(/(?<==)[\t\s]*/g, '')
+    .match(
+      /(?<name>(?<=[NAME] =)[\w\d]*);EXPNO =(?<expno>[\d]*);PROCNO =(?<procno>[\d]*)/,
+    );
+
+  const { expno, procno, name } = info?.groups || {};
+  const directory = text[2].replace(/\s*DU\s*=\t*([\w/.\d]+)/, '$1');
+
+  const integrals = [];
+  const integralData = text.slice(3).filter((t) => t);
+  for (let i = 1; i < integralData.length; i++) {
+    const data = integralData[i]
+      .replace(/^\s*/, '')
+      .replace(/[\s\t]+/g, ';')
+      .match(/\d+;(?<from>[0-9.]+);(?<to>[0-9.]+);(?<integration>[0-9.]+)/);
+    if (data) {
+      const { from, to, integration } = data.groups;
+      integrals.push({
+        from: parseFloat(from),
+        to: parseFloat(to),
+        integration: parseFloat(integration),
+      });
+    }
+  }
+
+  result.integrals = {
+    directory,
+    name,
+    expno: Number(expno),
+    procno: Number(procno),
+    integrals,
+  };
+}
+
 function joinInfoMeta(target, toAppend) {
@@ -406,2 +447,3 @@ for (let key in toAppend.meta) {
   if (files.quantFactorSample) addEreticFactor(result, files);
+  if (files.integrals) await addIntegrals(result, files);
 
@@ -408,0 +450,0 @@ if (files['1r'] || files['1i']) {

package.json

 {
   "name": "brukerconverter",
-  "version": "6.1.4",
+  "version": "6.1.5-pre.1691494258",
   "description": "Parse and convert Bruker raw data",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/__tests__/convertFileList.test.js

@@ -126,1 +126,26 @@ import { join } from 'path';
 });
+
+test('integrals.txt parsing', async () => {
+  const fileCollection = await fileCollectionFromPath(
+    join(__dirname, 'data/10'),
+  );
+  const results = await convertFileCollection(fileCollection);
+  expect(results).toHaveLength(2);
+  const pdata = results.find((result) => 'integrals' in result);
+  expect(pdata).toBeDefined();
+  expect(pdata.integrals).toEqual(
+    expect.objectContaining({
+      directory: '/opt/topspin4.3.0/examdata',
+      name: 'exam_CMCse_1',
+      procno: 1,
+      expno: 10,
+      integrals: expect.arrayContaining([
+        {
+          from: 6.633,
+          to: 6.56,
+          integration: 1,
+        },
+      ]),
+    }),
+  );
+});

src/__tests__/groupByExperiments.test.js

@@ -8,2 +8,12 @@ import { join } from 'path';
 
+test('integrals.txt parsing', async () => {
+  const fileCollection = await fileCollectionFromPath(
+    join(__dirname, 'data/10'),
+  );
+  const results = groupByExperiments(fileCollection);
+  expect(results).toHaveLength(2);
+  const pdata = results.find((result) => 'integrals' in result);
+  expect(pdata).toBeDefined();
+});
+
 test('groupByExperiment without expno', async () => {
@@ -10,0 +20,0 @@ const fileCollection = await fileCollectionFromPath(

src/groupByExperiments.js

@@ -71,3 +71,3 @@ /**
       processedData.fileCollectionItems.push(file); // check if it can be moved into the conditional block
-      if (file.name.match(/^(1r|1i|2rr|procs|proc2s)$/)) {
+      if (file.name.match(/^(1r|1i|2rr|procs|proc2s|integrals.txt)$/)) {
         processedData[file.name] = file;
@@ -167,2 +167,3 @@ }
         experimentsArray.push({
+          integrals: oneProcessed['integrals.txt'],
           acqus: experiment.acqus,
@@ -182,3 +183,2 @@ acqu2s: experiment.acqu2s,
   }
-
   return experimentsArray;
@@ -185,0 +185,0 @@ }

src/util/convert1D.js

@@ -0,1 +1,2 @@
+import { addIntegrals } from './addIntegrals.js';
 import { joinInfoMeta } from './joinMetaInfo.js';
@@ -12,2 +13,3 @@ import { parseData } from './parseData';
   if (files.quantFactorSample) addEreticFactor(result, files);
+  if (files.integrals) await addIntegrals(result, files);
 
@@ -14,0 +16,0 @@ if (files['1r'] || files['1i']) {

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

1729247

0.22%

Number of package files

49

4.26%

Lines of code

1907

6.24%

Worsened metrics

Number of low quality alerts

2

100%

No dependency changes