fix: correclty use inflate and not deflate

README.md

@@ -1,3 +1,24 @@
+# History of formats
+
+https://dx.doi.org/10.1074/mcp.R110.000133
+
+- mzData was developed by HUPO-PSI
+  - http://psidev.info/index.php?q
node/80#mzdata
+  - https://doi.org/10.1002/pmic.200300588
+- mzXML was developed at the Institute for Systems Biology
+- mzML: new unified output format started in 2006
+
+mzML - 4 goals:
+
+- creation of a simple format
+- elimination of alternate ways to encode the same information
+- support for all the features of both mzXML and mzData
+- validation through implementation prior to release.
+
+![mzml](images/mzml.png)
+
+cv = Controlled Volabulatry
+
 # mzData
 
 [![NPM version][npm-image]][npm-url]

package.json

@@ -33,14 +33,14 @@
     "testEnvironment": "node"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.23.3",
+    "@babel/plugin-transform-modules-commonjs": "^7.24.1",
     "@types/jest": "^29.5.12",
     "cheminfo-build": "^1.2.0",
     "eslint": "^8.57.0",
     "eslint-config-cheminfo": "^9.2.0",
     "jest": "^29.7.0",
     "prettier": "^3.2.5",
-    "rollup": "^4.12.0"
+    "rollup": "^4.17.2"
   },
   "dependencies": {
     "arraybuffer-xml-parser": "^0.6.0",

rollup.config.mjs

@@ -2,6 +2,6 @@ export default {
   input: 'src/index.js',
   output: {
     format: 'cjs',
-    file: 'lib/index.js'
+    file: 'lib/index.js',
   }
 };

src/mzml/parseMzML.js

@@ -6,6 +6,8 @@ import { processSpectrumList } from './processSpectrumList';
 
 const decoder = new TextDecoder();
 
+// https://www.psidev.info/mzml
+// CV = Controlled vocabulary
 export function parseMzML(arrayBuffer) {
   const result = {
     metadata: {},

src/mzml/utils.js

@@ -1,12 +1,12 @@
 import { decode } from 'base64-arraybuffer';
-import pako from 'pako';
+import { inflate } from 'pako';
 
 export function decoder(base64Encoded, options = {}) {
   const { compressionAlgorithm } = options;
   let decoded;
   switch (compressionAlgorithm) {
     case 'zlib':
-      decoded = pako.deflate(decode(base64Encoded));
+      decoded = inflate(decode(base64Encoded));
       break;
     case undefined:
     case '':

src/mzxml/utils.js

@@ -1,12 +1,12 @@
 import { decode } from 'base64-arraybuffer';
-import pako from 'pako';
+import { inflate } from 'pako';
 
 export function decoder(base64Encoded, options = {}) {
   const { compressionAlgorithm } = options;
   let decoded;
   switch (compressionAlgorithm) {
     case 'zlib':
-      decoded = pako.deflate(decode(base64Encoded));
+      decoded = inflate(decode(base64Encoded));
       break;
     case undefined:
     case '':

src/util/decodeBase64.js

@@ -1,4 +1,4 @@
-import pako from 'pako';
+import { inflate } from 'pako';
 import { decode } from 'uint8-base64';
 
 export function decodeBase64(base64, options = {}) {
@@ -28,13 +28,13 @@ export function decodeBase64(base64, options = {}) {
   let uint8Array = decode(base64);
   switch (compression.toLowerCase()) {
     case 'zlib':
-      uint8Array = pako.inflate(uint8Array);
+      uint8Array = inflate(uint8Array);
       break;
     case '':
     case 'none':
       break;
     default:
-      throw new Error(`Unknow compression algorithm: ${compression}`);
+      throw new Error(`Unknown compression algorithm: ${compression}`);
   }
 
   switch (endian.toLowerCase()) {