mzdata - npm Package Compare versions

Comparing version 2.0.1 to 2.1.0

History.md

@@ -0,1 +1,5 @@
+# [2.1.0](https://github.com/cheminfo-js/mzData/compare/v2.0.1...v2.1.0) (2020-04-20)
+
+
+
 ## [2.0.1](https://github.com/cheminfo-js/mzData/compare/v1.1.0...v2.0.1) (2020-02-28)
@@ -2,0 +6,0 @@

lib/index.js

@@ -205,2 +205,103 @@ 'use strict';
 
+function parseCvParam$2(cvParam) {
+  let result = {};
+  if (!cvParam) return result;
+  let cvParams;
+  if (Array.isArray(cvParam)) {
+    cvParams = cvParam;
+  } else {
+    cvParams = [cvParam];
+  }
+  for (let param of cvParams) {
+    if (param.precision) {
+      result = {
+        precision: param.precision,
+        byteOrder: param.byteOrder,
+        contentType: param.contentType,
+        pairOrder: param.pairOrder,
+      };
+    }
+  }
+  return result;
+}
+
+function parseBinaryDataArray$1(node) {
+  let data = node.peaks;
+  let attr = node._attr;
+  let cvParam = parseCvParam$2(data._attr);
+  if (!data || !attr) return [];
+  let buffer = decoder$1(data._data, cvParam);
+  let kind = '';
+  if (cvParam.contentType) {
+    kind = cvParam.contentType;
+  } else if (cvParam.pairOrder) {
+    kind = cvParam.pairOrder;
+  } else {
+    throw new Error('unknown binary data type');
+  }
+  // console.log(buffer)
+  if (cvParam.precision === 64) {
+    let result = {};
+    result.data = new Float64Array(buffer.buffer);
+    result.kind = kind;
+    return result;
+  } else if (cvParam.precision === 32) {
+    let result = {};
+    result.data = new Float32Array(buffer);
+    result.kind = kind;
+    return result;
+  }
+  throw new Error(`unknown precision in decoder: ${attr.precision}`);
+}
+
+function decoder$1(base64Encoded, cvParams = {}) {
+  if (cvParams.compressionType === 'zlib') {
+    return pako.inflate(base64Js.toByteArray(base64Encoded));
+  } else {
+    return base64Js.toByteArray(base64Encoded);
+  }
+}
+
+function processSpectrumList$2(parsed, msData) {
+  if (!parsed.msRun.scan) return;
+  let scanList = parsed.msRun.scan;
+  if (Array.isArray(scanList) === false) scanList = [scanList];
+  if (scanList[0]._attr) {
+    msData.info = [];
+  }
+  for (let scan of scanList) {
+    if (typeof scan !== 'object') continue;
+    if (Array.isArray(scan)) {
+      throw new Error('processSpectrumList: scan may not be an array');
+    }
+    let dataArray = parseBinaryDataArray$1(scan);
+    let first = new Float64Array(dataArray.data.length / 2);
+    let second = new Float64Array(dataArray.data.length / 2);
+    for (let i = 0; i < dataArray.data.length / 2; i++) {
+      first[i] = dataArray.data[i * 2];
+      second[i] = dataArray.data[i * 2 + 1];
+    }
+    msData.data.push([first, second]);
+    msData.info.push(scan._attr);
+  }
+}
+
+function processMZXML(topLevel, result) {
+  processSpectrumList$2(topLevel, result.series.ms);
+  let offset = topLevel.index.offset;
+  for (let i = 0; i < offset.length; i++) {
+    let index = offset[i]._attr.id;
+    let data = offset[i]._data;
+    result.times[index - 1] = data;
+  }
+  result.metadata = {
+    msManufacturer: topLevel.msRun.msInstrument.msManufacturer._attr,
+    msModel: topLevel.msRun.msInstrument.msModel._attr,
+    msIonisation: topLevel.msRun.msInstrument.msIonisation._attr,
+    msMassAnalyzer: topLevel.msRun.msInstrument.msMassAnalyzer._attr,
+    msDetector: topLevel.msRun.msInstrument.msDetector._attr,
+    software: topLevel.msRun.msInstrument.software._attr,
+  };
+}
+
 function ensureText(data, options = {}) {
@@ -271,2 +372,3 @@ const { encoding = 'utf8' } = options;
     case 'mzxml':
+      processMZXML(topLevel.mzxml, result);
       break;
@@ -273,0 +375,0 @@ default:

package.json

 {
   "name": "mzdata",
-  "version": "2.0.1",
+  "version": "2.1.0",
   "description": "Read and explore mzData v1.05 files",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/index.js

@@ -5,2 +5,3 @@ import { parse } from 'fast-xml-parser';
 import { processMZML } from './mzml/process';
+import { processMZXML } from './mzxml/process';
 import { ensureText } from './util/ensureText';
@@ -50,2 +51,3 @@ import { searchObjectKey } from './util/searchObjectKey';
     case 'mzxml':
+      processMZXML(topLevel.mzxml, result);
       break;
@@ -52,0 +54,0 @@ default:

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Found 1 instance in 1 package

Fixed alerts

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Improved metrics

Total package byte prevSize

35588

increased by37.25%

Number of package files

27

increased by28.57%

Lines of code

951

increased by46.08%

Worsened metrics

Number of low supply chain risk alerts

3

increased by50%

No dependency changes