mzdata - npm Package Compare versions

Comparing version 1.0.1 to 1.1.0

History.md

@@ -0,1 +1,6 @@
+<a name="1.1.0"></a>
+# [1.1.0](https://github.com/cheminfo-js/mzData/compare/v1.0.1...v1.1.0) (2018-10-25)
+
+
+
 <a name="1.0.1"></a>
@@ -2,0 +7,0 @@ ## [1.0.1](https://github.com/cheminfo-js/mzData/compare/v0.2.0...v1.0.1) (2018-10-22)

package.json

 {
   "name": "mzdata",
-  "version": "1.0.1",
+  "version": "1.1.0",
   "description": "Read and explore mzData v1.05 files",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "src/index.js",
+  "browser": {
+    "./src/util/ensureText.js": "./src/util/ensureTextBrowser.js"
+  },
   "files": [
-    "lib",
     "src"
@@ -14,7 +15,6 @@ ],
     "eslint-fix": "npm run eslint -- --fix",
-    "prepublish": "rollup -c",
     "test": "run-s testonly eslint",
     "test-travis": "eslint src && jest --coverage && codecov",
     "testonly": "jest",
-    "build": "rollup -c && cheminfo build"
+    "build": "cheminfo build"
   },
@@ -26,3 +26,3 @@ "repository": {
   "keywords": [],
-  "author": "Miguel Asencio",
+  "author": "Miguel Asencio, Luc Patiny",
   "license": "MIT",
@@ -37,3 +37,2 @@ "bugs": {
   "devDependencies": {
-    "babel-plugin-transform-es2015-modules-commonjs": "^6.24.1",
     "cheminfo-tools": "^1.17.1",
@@ -43,4 +42,5 @@ "codecov": "^2.2.0",
     "eslint-config-cheminfo": "^1.8.0",
+    "eslint-plugin-import": "^2.14.0",
+    "eslint-plugin-jest": "^21.26.1",
     "eslint-plugin-no-only-tests": "^2.0.0",
-    "esm": "^3.0.84",
     "jest": "^21.2.1",
@@ -51,5 +51,5 @@ "npm-run-all": "^4.0.2",
   "dependencies": {
-    "base64-js": "^1.2.1",
-    "sax": "^1.2.4"
+    "base64-js": "^1.3.0",
+    "fast-xml-parser": "^3.12.5"
   }
 }

src/index.js

@@ -1,79 +0,46 @@
-import {parser} from 'sax';
-import {decoder, mergeSeries} from './utils';
+'use strict';
 
+const FastXmlParser = require('fast-xml-parser');
+
+const processMetadata = require('./processMetaData');
+const processSpectrumList = require('./processSpectrumList');
+const ensureText = require('./util/ensureText');
+
 /**
  * Reads a mzData v1.05 file
- * @param {ArrayBuffer} data - ArrayBuffer or any Typed Array (including Node.js' Buffer from v4) with the data
+ * @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>>}}}}
  */
-export default function mzData(data) {
-    const xml = parser(true, {trim: true});
+function mzData(xml) {
+  xml = ensureText(xml);
 
-    var result = {
-        times: [],
-        series: {}
-    };
-    var error = [];
-    var binaryData = {};
-    var mz = [];
-    var int = [];
-    var kind;
+  if (typeof xml !== 'string') throw new Error('Unknown variable type');
 
-    xml.onopentag = (node) => {
-        // eslint-disable-next-line default-case
-        switch (node.name) {
-            case 'mzData':
-                kind = 'mzData';
-                break;
-            case 'cvParam':
-                if (node.attributes.name === 'TimeInMinutes') {
-                    result.times.push(Number(node.attributes.value));
-                }
-                break;
-            case 'mzArrayBinary':
-                binaryData = {
-                    serie: 'mz'
-                };
-                break;
-            case 'intenArrayBinary':
-                binaryData = {
-                    serie: 'int'
-                };
-                break;
-            case 'data':
-                if (node.isSelfClosing) {
-                    if (binaryData.serie === 'mz') {
-                        mz.push([]);
-                    } else if (binaryData.serie === 'int') {
-                        int.push([]);
-                    }
-                    binaryData = {};
-                } else if (binaryData.serie) {
-                    binaryData.precision = node.attributes.precision;
-                }
-                break;
-        }
-    };
+  let parsed = FastXmlParser.parse(xml, {
+    textNodeName: '_data',
+    attributeNamePrefix: '',
+    parseAttributeValue: true,
+    attrNodeName: '_attr',
+    ignoreAttributes: false
+  });
 
-    xml.ontext = (raw) => {
-        if (binaryData.serie === 'mz') {
-            mz.push(decoder(raw, binaryData));
-        } else if (binaryData.serie === 'int') {
-            int.push(decoder(raw, binaryData));
-        }
-        binaryData = {};
-    };
+  if (!parsed.mzData) throw new Error('The parent node is not mzData');
 
-    xml.onerror = (err) => error.push(err);
-    xml.write(data).close();
-    if (!kind || kind !== 'mzData') {
-        throw new TypeError('Not a mzData file');
+  let result = {
+    metadata: {},
+    times: [],
+    series: {
+      ms: {
+        data: []
+      }
     }
-    if (error.length > 0) {
-        throw new Error(error);
-    }
+  };
 
-    result.series.ms = {};
-    result.series.ms.data = mergeSeries(mz, int);
-    return result;
+  processMetadata(parsed.mzData, result.metadata);
+
+  processSpectrumList(parsed.mzData, result.times, result.series.ms.data);
+
+  return result;
 }
+
+module.exports = mzData;

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License

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Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

Fixed 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

Improved metrics

Number of package files

12

increased by50%

Worsened metrics

Total package byte prevSize

10290

decreased by-0.76%

Lines of code

184

decreased by-8.46%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• + Addedfast-xml-parser@^3.12.5

• + Addedfast-xml-parser@3.21.1(transitive)

• + Addedstrnum@1.0.5(transitive)

• - Removedsax@^1.2.4

• - Removedsax@1.4.1(transitive)

• Updatedbase64-js@^1.3.0