mzdata - npm Package Compare versions

Comparing version 2.3.2 to 3.0.0

lib/index.js

 'use strict';
 
 var arraybufferXmlParser = require('arraybuffer-xml-parser');
-var pako = require('pako');
+var mlSpectraProcessing = require('ml-spectra-processing');
 var uint8Base64 = require('uint8-base64');
 var camelCase = require('camelcase');
 
-function decodeBase64(base64, options = {}) {
+async function inflate(zlibCompressedData) {
+  const inputStream = new ReadableStream({
+    start(controller) {
+      controller.enqueue(zlibCompressedData);
+      controller.close();
+    },
+  });
+
+  const decompressedStream = inputStream.pipeThrough(
+    new DecompressionStream('deflate'),
+  );
+
+  const reader = decompressedStream.getReader();
+  const chunks = [];
+  let totalLength = 0;
+
+  while (true) {
+    // eslint-disable-next-line no-await-in-loop
+    const { value, done } = await reader.read();
+    if (done) break;
+    chunks.push(value);
+    totalLength += value.length;
+  }
+
+  // Combine chunks into a single Uint8Array
+  const decompressedData = new Uint8Array(totalLength);
+  let offset = 0;
+  for (const chunk of chunks) {
+    decompressedData.set(chunk, offset);
+    offset += chunk.length;
+  }
+
+  return decompressedData;
+}
+
+async function decodeBase64(base64, options = {}) {
   let {
@@ -35,3 +70,3 @@ endian = 'little',
     case 'zlib':
-      uint8Array = pako.inflate(uint8Array);
+      uint8Array = await inflate(uint8Array);
       break;
@@ -175,3 +210,10 @@ case '':
 
-function parseMzData(arrayBuffer) {
+/**
+ *
+ * @param {*} arrayBuffer
+ * @param {import('../Options.js').Options} [options={}]
+ * @returns
+ */
+async function parseMzData(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -188,10 +230,16 @@ metadata: {},
   let parsed = arraybufferXmlParser.parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
       if (node.tagName !== 'data') return decoder$3.decode(value);
-      return decodeBase64(node.value, node.attributes);
+      const promise = decodeBase64(node.bytes, node.attributes);
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
-
+  await mlSpectraProcessing.recursiveResolve(parsed);
   processMetadata(parsed.mzData, result.metadata);
@@ -276,3 +324,4 @@ processSpectrumList$2(parsed.mzData, result.times, result.series.ms.data);
 // CV = Controlled vocabulary
-function parseMzML(arrayBuffer) {
+async function parseMzML(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -289,4 +338,4 @@ metadata: {},
   let parsed = arraybufferXmlParser.parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
@@ -297,6 +346,13 @@ if (node.tagName !== 'binary') return decoder$2.decode(value);
       );
-
-      return decodeBase64(node.value, { ontologies });
+      const promise = decodeBase64(node.bytes, { ontologies });
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
+  // parsed file still contains promises
+  await mlSpectraProcessing.recursiveResolve(parsed);
 
@@ -340,3 +396,10 @@ const mzML = parsed.mzML || parsed.indexedmzML.mzML;
 
-function parseMzXML(arrayBuffer) {
+/**
+ *
+ * @param {*} arrayBuffer
+ * @param {import('../Options.js').Options} [options]
+ * @returns
+ */
+async function parseMzXML(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -352,7 +415,8 @@ metadata: {},
   let parsed = arraybufferXmlParser.parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
       if (node.tagName !== 'peaks') return decoder$1.decode(value);
-      return decodeBase64(node.value, {
+
+      const promise = decodeBase64(node.bytes, {
         precision: node.attributes.precision,
@@ -362,4 +426,11 @@ endian: node.attributes.byteOrder,
       });
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
+  await mlSpectraProcessing.recursiveResolve(parsed);
 
@@ -376,5 +447,6 @@ processSpectrumList(parsed.mzXML, result.times, result.series.ms);
  * @param {ArrayBuffer|string} xml - ArrayBuffer or String or any Typed Array (including Node.js' Buffer from v4) with the data
- * @return {{times: Array<number>, series: { ms: { data:Array<Array<number>>}}}}
+ * @param {import('./Options.js').Options} [options={}]
+ * @return Promise<{{times: Array<number>, series: { ms: { data:Array<Array<number>>}}}}>
  */
-function parseMZ(xml) {
+async function parseMZ(xml, options = {}) {
   if (typeof xml === 'string') {
@@ -394,7 +466,7 @@ const encoder = new TextEncoder();
   if (header.includes('mzData')) {
-    return parseMzData(xml);
+    return parseMzData(xml, options);
   } else if (header.includes('mzML')) {
-    return parseMzML(xml);
+    return parseMzML(xml, options);
   } else if (header.includes('mzXML')) {
-    return parseMzXML(xml);
+    return parseMzXML(xml, options);
   } else {
@@ -401,0 +473,0 @@ throw new Error(`MZ parser: unknown format`);

package.json

 {
   "name": "mzdata",
-  "version": "2.3.2",
+  "version": "3.0.0",
   "description": "Read and explore mzData v1.05 files",
@@ -34,3 +34,3 @@ "main": "lib/index.js",
     "@babel/plugin-transform-modules-commonjs": "^7.25.9",
-    "@vitest/coverage-v8": "2.1.7",
+    "@vitest/coverage-v8": "2.1.8",
     "cheminfo-build": "^1.2.0",
@@ -42,11 +42,11 @@ "eslint": "^9.16.0",
     "rollup": "^4.28.0",
-    "vitest": "^2.1.7"
+    "vitest": "^2.1.8"
   },
   "dependencies": {
-    "arraybuffer-xml-parser": "^0.6.1",
-    "base64-arraybuffer": "^1.0.2",
+    "arraybuffer-xml-parser": "^1.0.0",
     "camelcase": "^6.3.0",
-    "pako": "^2.1.0",
+    "cheminfo-types": "^1.8.1",
+    "ml-spectra-processing": "^14.8.0",
     "uint8-base64": "^0.1.1"
   }
 }

README.md

@@ -48,3 +48,3 @@ # History of formats
 const mzDataFile = readFileSync(__dirname + '/tiny.mzData.xml');
-var response = parseMZ(mzDataFile);
+var response = await parseMZ(mzDataFile);
 ```
@@ -62,4 +62,2 @@
 
-## [API Documentation](https://cheminfo-js.github.io/mzData/)
-
 ## License
@@ -66,0 +64,0 @@

src/index.js

@@ -10,5 +10,6 @@ import { parseMzData } from './mzdata/parseMzData';
  * @param {ArrayBuffer|string} xml - ArrayBuffer or String or any Typed Array (including Node.js' Buffer from v4) with the data
- * @return {{times: Array<number>, series: { ms: { data:Array<Array<number>>}}}}
+ * @param {import('./Options.js').Options} [options={}]
+ * @return Promise<{{times: Array<number>, series: { ms: { data:Array<Array<number>>}}}}>
  */
-export function parseMZ(xml) {
+export async function parseMZ(xml, options = {}) {
   if (typeof xml === 'string') {
@@ -28,7 +29,7 @@ const encoder = new TextEncoder();
   if (header.includes('mzData')) {
-    return parseMzData(xml);
+    return parseMzData(xml, options);
   } else if (header.includes('mzML')) {
-    return parseMzML(xml);
+    return parseMzML(xml, options);
   } else if (header.includes('mzXML')) {
-    return parseMzXML(xml);
+    return parseMzXML(xml, options);
   } else {
@@ -35,0 +36,0 @@ throw new Error(`MZ parser: unknown format`);

src/mzdata/parseMzData.js

 import { parse } from 'arraybuffer-xml-parser';
+import { recursiveResolve } from 'ml-spectra-processing';
 
@@ -10,3 +11,10 @@ import { decodeBase64 } from '../util/decodeBase64';
 
-export function parseMzData(arrayBuffer) {
+/**
+ *
+ * @param {*} arrayBuffer
+ * @param {import('../Options.js').Options} [options={}]
+ * @returns
+ */
+export async function parseMzData(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -23,10 +31,16 @@ metadata: {},
   let parsed = parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
       if (node.tagName !== 'data') return decoder.decode(value);
-      return decodeBase64(node.value, node.attributes);
+      const promise = decodeBase64(node.bytes, node.attributes);
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
-
+  await recursiveResolve(parsed);
   processMetadata(parsed.mzData, result.metadata);
@@ -33,0 +47,0 @@ processSpectrumList(parsed.mzData, result.times, result.series.ms.data);

src/mzml/parseMzML.js

 import { parse } from 'arraybuffer-xml-parser';
+import { recursiveResolve } from 'ml-spectra-processing';
 
@@ -11,3 +12,4 @@ import { decodeBase64 } from '../util/decodeBase64';
 // CV = Controlled vocabulary
-export function parseMzML(arrayBuffer) {
+export async function parseMzML(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -24,4 +26,4 @@ metadata: {},
   let parsed = parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
@@ -32,6 +34,13 @@ if (node.tagName !== 'binary') return decoder.decode(value);
       );
-
-      return decodeBase64(node.value, { ontologies });
+      const promise = decodeBase64(node.bytes, { ontologies });
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
+  // parsed file still contains promises
+  await recursiveResolve(parsed);
 
@@ -38,0 +47,0 @@ const mzML = parsed.mzML || parsed.indexedmzML.mzML;

src/mzml/utils.js

@@ -1,5 +0,6 @@
-import { decode } from 'base64-arraybuffer';
-import { inflate } from 'pako';
+import { decode } from 'uint8-base64';
 
-export function decoder(base64Encoded, options = {}) {
+import { inflate } from '../util/inflate.js';
+
+export async function decoder(base64Encoded, options = {}) {
   const { compressionAlgorithm } = options;
@@ -9,3 +10,3 @@ let decoded;
     case 'zlib':
-      decoded = inflate(decode(base64Encoded));
+      decoded = await inflate(decode(base64Encoded));
       break;
@@ -21,3 +22,3 @@ case undefined:
   }
-  if (!decoded.byteLength % 8) {
+  if (decoded.length % 8 !== 0) {
     throw new Error('decode to Float64Array not the right length');
@@ -24,0 +25,0 @@ }

src/mzxml/parseMzXML.js

 import { parse } from 'arraybuffer-xml-parser';
+import { recursiveResolve } from 'ml-spectra-processing';
 
@@ -9,3 +10,10 @@ import { decodeBase64 } from '../util/decodeBase64';
 
-export function parseMzXML(arrayBuffer) {
+/**
+ *
+ * @param {*} arrayBuffer
+ * @param {import('../Options.js').Options} [options]
+ * @returns
+ */
+export async function parseMzXML(arrayBuffer, options = {}) {
+  const { logger = console } = options;
   const result = {
@@ -21,7 +29,8 @@ metadata: {},
   let parsed = parse(arrayBuffer, {
-    attributeNamePrefix: '',
     attributesNodeName: 'attributes',
+    attributeNameProcessor: (attributeName) => attributeName,
     tagValueProcessor: (value, node) => {
       if (node.tagName !== 'peaks') return decoder.decode(value);
-      return decodeBase64(node.value, {
+
+      const promise = decodeBase64(node.bytes, {
         precision: node.attributes.precision,
@@ -31,4 +40,11 @@ endian: node.attributes.byteOrder,
       });
+      // avoid unhandled promise rejection and swallow the error
+      promise.catch((error) => {
+        logger.error('error decoding base64', error);
+        return [];
+      });
+      return promise;
     },
   });
+  await recursiveResolve(parsed);
 
@@ -35,0 +51,0 @@ processSpectrumList(parsed.mzXML, result.times, result.series.ms);

src/mzxml/utils.js

@@ -1,5 +0,6 @@
-import { decode } from 'base64-arraybuffer';
-import { inflate } from 'pako';
+import { decode } from 'uint8-base64';
 
-export function decoder(base64Encoded, options = {}) {
+import { inflate } from '../util/inflate.js';
+
+export async function decoder(base64Encoded, options = {}) {
   const { compressionAlgorithm } = options;
@@ -9,3 +10,3 @@ let decoded;
     case 'zlib':
-      decoded = inflate(decode(base64Encoded));
+      decoded = await inflate(decode(base64Encoded));
       break;
@@ -21,3 +22,3 @@ case undefined:
   }
-  if (!decoded.byteLength % 8) {
+  if (decoded.byteLength % 8 !== 0) {
     throw new Error('decode to Float64Array not the right length');
@@ -24,0 +25,0 @@ }

src/util/decodeBase64.js

@@ -1,5 +0,6 @@
-import { inflate } from 'pako';
 import { decode } from 'uint8-base64';
 
-export function decodeBase64(base64, options = {}) {
+import { inflate } from './inflate.js';
+
+export async function decodeBase64(base64, options = {}) {
   let {
@@ -31,3 +32,3 @@ endian = 'little',
     case 'zlib':
-      uint8Array = inflate(uint8Array);
+      uint8Array = await inflate(uint8Array);
       break;
@@ -34,0 +35,0 @@ case '':

New alerts

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License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

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This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

7823423

increased by0.06%

Number of package files

22

increased by10%

Lines of code

977

increased by17.01%

Worsened metrics

Number of lines in readme file

73

decreased by-2.67%

Dependency changes

• + Addedcheminfo-types@^1.8.1

• + Addedml-spectra-processing@^14.8.0

• + Addedarraybuffer-xml-parser@1.0.0(transitive)

• + Addedbinary-search@1.3.6(transitive)

• + Addedcheminfo-types@1.8.1(transitive)

• + Addedd3-array@0.7.1(transitive)

• + Addedfft.js@4.0.4(transitive)

• + Addedis-any-array@2.0.1(transitive)

• + Addedml-array-max@1.2.4(transitive)

• + Addedml-array-min@1.2.3(transitive)

• + Addedml-array-rescale@1.3.7(transitive)

• + Addedml-matrix@6.12.0(transitive)

• + Addedml-spectra-processing@14.9.1(transitive)

• + Addedml-xsadd@3.0.1(transitive)

• + Addedspline-interpolator@1.0.0(transitive)

• - Removedbase64-arraybuffer@^1.0.2

• - Removedpako@^2.1.0

• - Removedarraybuffer-xml-parser@0.6.1(transitive)

• - Removedbase64-arraybuffer@1.0.2(transitive)

• - Removedpako@2.1.0(transitive)

• Updatedarraybuffer-xml-parser@^1.0.0