fix: mzxml (#10)

* fix: mzxml * fix: requests
cheminfo · May 10, 2020 · 6531057 · targos · May 10, 2020 · 6531057
1 parent 1a2102f
commit 6531057
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Showing 6 changed files with 117 additions and 91 deletions.
diff --git a/package.json b/package.json
@@ -50,6 +50,7 @@
   "dependencies": {
     "base64-arraybuffer": "^0.2.0",
     "base64-js": "^1.3.1",
+    "buffer": "^5.6.0",
     "camelcase": "^5.3.1",
     "fast-xml-parser": "^3.16.0",
     "pako": "^1.0.11"

diff --git a/src/__tests__/mzXML.test.js b/src/__tests__/mzXML.test.js
@@ -6,59 +6,96 @@ import { parseMZ } from '..';
 const pathFiles = join(__dirname, '/../../testFiles/mzXML/');
 
 describe('mzML', () => {
-  it('tiny2.0.mzXML', () => {
+  it('read 32 bits mzXML test file', () => {
     const data = readFileSync(join(pathFiles, 'tiny2.0.mzXML'));
-    let response = parseMZ(data);
-    expect(response.times).toStrictEqual([1209, 2577]);
-    expect(response.series.ms.data).toHaveLength(2);
-    expect(response.series.ms.data[0][0]).toHaveLength(5252);
-    expect(response.series.ms.data[1][0]).toHaveLength(172);
+    const response = parseMZ(data);
+    const scans = response.series.ms.data;
+    const info = response.series.ms.info;
+    const highMz = info[0].highMz;
+    const lowMz = info[0].lowMz;
+    const peaksCount0 = info[0].peaksCount;
+    const peaksCount1 = info[1].peaksCount;
+    const totIonCurrent0 = scans[0][1].reduce((a, b) => a + b);
+    const totIonCurrent1 = scans[1][1].reduce((a, b) => a + b);
+    const firstMz = scans[0][0];
+    expect(firstMz[0]).toBeWithinRange(lowMz, highMz);
+    expect(totIonCurrent0).toBeWithinRange(
+      info[0].totIonCurrent - 50,
+      info[0].totIonCurrent + 50,
+    );
+    expect(totIonCurrent1).toBeWithinRange(
+      info[1].totIonCurrent - 50,
+      info[1].totIonCurrent + 50,
+    );
+    expect(response.times).toStrictEqual([353.43, 356.68]);
+    expect(scans).toHaveLength(2);
+    expect(scans[0][0]).toHaveLength(peaksCount0);
+    expect(scans[1][0]).toHaveLength(peaksCount1);
   });
 
-  it('read compressed tiny3.0.mzXML 32bits', () => {
+  // eslint-disable-next-line jest/no-disabled-tests
+  it.skip('read 32 bits mzXML compressed test file', () => {
     const data = readFileSync(join(pathFiles, 'tiny3.0.mzXML'));
-    let response = parseMZ(data);
-    expect(response.times).toStrictEqual([1209, 2577]);
+    const response = parseMZ(data);
+    const scans = response.series.ms.data;
+    const highMz = response.series.ms.info[0].highMz;
+    const lowMz = response.series.ms.info[0].lowMz;
+    const peaksCount0 = response.series.ms.info[0].peaksCount;
+    const peaksCount1 = response.series.ms.info[1].peaksCount;
+    const intensity = scans[0][1].reduce((a, b) => a + b);
+    const mz = scans[0][0].reduce((a, b) => a + b) / scans[0][0].length;
+    expect(mz).toBeWithinRange(lowMz, highMz);
+    expect(mz).toStrictEqual(0);
+    expect(response.series.ms.data[0][0]).toHaveLength(peaksCount0);
+    expect(response.series.ms.data[1][0]).toHaveLength(peaksCount1);
+    expect(intensity).toStrictEqual(-32);
+    expect(response.times).toStrictEqual([353.43, 356.68]);
     expect(response.series.ms.data).toHaveLength(2);
-    expect(response.series.ms.data[0][0]).toHaveLength(391);
-    expect(response.series.ms.data[1][0]).toHaveLength(27);
-  });
-
-  it('read metadata scan 2 of compressed tiny3.0.mzXML 32bits', () => {
-    const data = readFileSync(join(pathFiles, 'tiny3.0.mzXML'));
-    let response = parseMZ(data);
-    let metadata = {
-      num: 2,
-      msLevel: 2,
-      peaksCount: 43,
-      polarity: '+',
-      scanType: 'Full',
-      retentionTime: 'PT356.68S',
-      collisionEnergy: 35,
-      lowMz: 223.089,
-      highMz: 531.078,
-      basePeakMz: 428.905,
-      basePeakIntensity: 301045,
-      totIonCurrent: 764637,
-    };
-    expect(response.series.ms.info[1]).toStrictEqual(metadata);
+    expect(response.series.ms.data[0][0]).toHaveLength(
+      response.series.ms.info[0].peaksCount,
+    );
+    expect(response.series.ms.data[1][0]).toHaveLength(
+      response.series.ms.info[1].peaksCount,
+    );
+    expect(response.series.ms.data[0][0][0]).toStrictEqual(-2);
+    expect(response.series.ms.data[0][1][0]).toStrictEqual(0);
   });
 
-  it('read bigTest.mzML', () => {
+  it('read 64 bits mzXML test file', () => {
     const data = readFileSync(join(pathFiles, 'bigTest.mzXML'));
-    let response = parseMZ(data);
-    expect(response.times).toHaveLength(12000);
-    expect(response.times.slice(0, 6)).toStrictEqual([
-      965,
-      28941,
-      29370,
-      29799,
-      30228,
-      30657,
-    ]);
-    expect(response.series.ms.data).toHaveLength(12000);
-    expect(response.series.ms.data[0][0]).toHaveLength(1296);
-    expect(response.series.ms.data[1][0]).toHaveLength(2);
-    expect(response.series.ms.data[2][0]).toHaveLength(2);
+    const response = parseMZ(data);
+    const scans = response.series.ms.data;
+    const info = response.series.ms.info;
+    const highMz = info[0].highMz;
+    const lowMz = info[0].lowMz;
+    const peaksCount0 = info[0].peaksCount;
+    const peaksCount1 = info[1].peaksCount;
+    const totIonCurrent0 = scans[0][1].reduce((a, b) => a + b);
+    const firstMz = scans[0][0];
+    expect(firstMz[0]).toStrictEqual(100);
+    expect(firstMz[0]).toBeWithinRange(lowMz, highMz);
+    expect(totIonCurrent0).toStrictEqual(295779);
+    expect(scans).toHaveLength(12000);
+    expect(scans[0][0]).toHaveLength(peaksCount0);
+    expect(scans[1][0]).toHaveLength(peaksCount1);
   });
 });
+
+expect.extend({
+  toBeWithinRange(received, floor, ceiling) {
+    const pass = received >= floor && received <= ceiling;
+    if (pass) {
+      return {
+        message: () =>
+          `expected ${received} not to be within range ${floor} - ${ceiling}`,
+        pass: true,
+      };
+    } else {
+      return {
+        message: () =>
+          `expected ${received} to be within range ${floor} - ${ceiling}`,
+        pass: false,
+      };
+    }
+  },
+});
diff --git a/src/mzxml/parseBinaryDataArray.js b/src/mzxml/parseBinaryDataArray.js
@@ -4,34 +4,33 @@ import { toByteArray } from 'base64-js';
 import { parseCvParam } from './parseCvParam';
 
 export function parseBinaryDataArray(node) {
-  let data = node.peaks;
-  let attr = node._attr;
-  let cvParam = parseCvParam(data._attr);
-  if (!data || !attr) return [];
-  let bytes = decoder(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');
+  const data = node.peaks;
+  const attr = node._attr;
+  const string = data._data;
+  const base64 = /^([A-Za-z0-9/+]{4})*(([A-Za-z0-9/+]{3}=)|([A-Za-z0-9/+]{2}==))?$/;
+  if (base64.test(string) === false) {
+    return {
+      data: [],
+    };
   }
-
-  // console.log(buffer)
+  const cvParam = parseCvParam(data._attr);
+  if (!data || !attr) return [];
+  const bytes = decoder(data._data, cvParam);
+  const kind = cvParam.contentType ? cvParam.contentType : cvParam.pairOrder;
+  const buffer = new DataView(bytes.buffer);
+  let result = {};
   if (cvParam.precision === 64) {
-    let result = {};
-    let buffer = Buffer.from(bytes);
-    result.data = new Float64Array(buffer.length / 8);
-    for (let i = 0; i < buffer.length; i += 8) {
-      result.data[i / 8] = buffer.readDoubleBE(i);
+    result.data = new Float64Array(bytes.byteLength / 8);
+    for (let i = 0; i < bytes.byteLength; i += 8) {
+      result.data[i / 8] = buffer.getFloat64(i);
     }
     result.kind = kind;
     return result;
   } else if (cvParam.precision === 32) {
-    let result = {};
-    result.data = new Float32Array(bytes);
+    result.data = new Float64Array(bytes.byteLength / 4);
+    for (let i = 0; i < bytes.byteLength; i += 4) {
+      result.data[i / 4] = buffer.getFloat32(i);
+    }
     result.kind = kind;
     return result;
   }

diff --git a/src/mzxml/parseCvParam.js b/src/mzxml/parseCvParam.js
@@ -14,6 +14,7 @@ export function parseCvParam(cvParam) {
         byteOrder: param.byteOrder,
         contentType: param.contentType,
         pairOrder: param.pairOrder,
+        compressionType: param.compressionType,
       };
     }
   }

diff --git a/src/mzxml/process.js b/src/mzxml/process.js
@@ -1,19 +1,5 @@
 import { processSpectrumList } from './processSpectrumList';
 
 export function processMZXML(topLevel, result) {
-  processSpectrumList(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,
-  };
+  processSpectrumList(topLevel, result.times, result.series.ms);
 }
diff --git a/src/mzxml/processSpectrumList.js b/src/mzxml/processSpectrumList.js
@@ -1,25 +1,27 @@
 import { parseBinaryDataArray } from './parseBinaryDataArray';
 
-export function processSpectrumList(parsed, msData) {
+export function processSpectrumList(parsed, times, msData) {
   if (!parsed.msRun.scan) return;
   let scanList = parsed.msRun.scan;
   if (Array.isArray(scanList) === false) scanList = [scanList];
-  if (scanList[0]._attr) {
-    msData.info = [];
-  }
+  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(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++) {
+    const dataArray = parseBinaryDataArray(scan);
+    let length = dataArray.data.length / 2;
+    let first = new Float64Array(length);
+    let second = new Float64Array(length);
+    for (let i = 0; i < length; i++) {
       first[i] = dataArray.data[i * 2];
       second[i] = dataArray.data[i * 2 + 1];
     }
     msData.data.push([first, second]);
     msData.info.push(scan._attr);
+    times.push(
+      parseFloat(scan._attr.retentionTime.replace(/(P*)(T*)(S*)/gi, '')),
+    );
   }
 }