emdb - npm Package Compare versions

Comparing version 2.3.0 to 2.4.0

lib/index.js

@@ -20,3 +20,2 @@ 'use strict';
 var peaksSimilarity = require('peaks-similarity');
-var chemicalElements = require('chemical-elements');
 var Regression = require('ml-regression-theil-sen');
@@ -1024,224 +1023,3 @@ var mlSpectraProcessing = require('ml-spectra-processing');
 
-async function fetchJSON(url) {
-  const result = await crossFetch__default["default"](url);
-  return result.json();
-}
-
 /**
- * Generates a database 'pubchem' based on all molecular formula available
- * in the database and a monoisotopic mass.
- * @param {number|string|number[]} masses - Observed monoisotopic mass
- * @param {object} [options={}]
- * @param {string} [options.databaseName='pubchem']
- * @param {string} [options.ionizations=''] - string containing a comma separated list of modifications
- * @param {number} [options.precision=1000] - Precision of the monoisotopic mass in ppm
- * @param {string} [options.ranges=''] -
- * @param {number} [options.limit=1000] - Maximal number of entries to return
- * @param {number} [options.minPubchemEntries=5] - Minimal number of molecules having a specific MF
- * @param {string} [options.url='https://pubchem.cheminfo.org/mfs/v1/fromEM'] - URL of the webservice
- */
-
-async function searchPubchem(masses, options = {}) {
-  const {
-    url = 'https://pubchem.cheminfo.org/mfs/v1/fromEM',
-    precision = 1000,
-    limit = 1000,
-    ranges = '',
-    minPubchemEntries = 5,
-  } = options;
-
-  if (typeof masses === 'number') {
-    masses = [masses];
-  }
-  if (typeof masses === 'string') {
-    masses = masses.split(/[\r\n\t,; ]+/).map(Number);
-  }
-
-  let allowedEMs;
-  if (ranges) {
-    const allowedEMsArray = [];
-    for (let mass of masses) {
-      (
-        await mfFinder.findMFs(mass, {
-          ionizations: options.ionizations,
-          precision,
-          ranges,
-          limit: 100000,
-        })
-      ).mfs.forEach((mf) => allowedEMsArray.push(mf.em));
-    }
-    allowedEMs = Float64Array.from(allowedEMsArray).sort();
-  }
-  let promises = [];
-  let ionizations = mfUtilities.preprocessIonizations(options.ionizations);
-  for (let mass of masses) {
-    for (let ionization of ionizations) {
-      let realMass =
-        mass * Math.abs(ionization.charge || 1) -
-        ionization.em +
-        chemicalElements.ELECTRON_MASS * ionization.charge;
-      const pubchemURL = `${url}?em=${realMass}&precision=${precision}&limit=${limit}&minPubchemEntries=${minPubchemEntries}`;
-      promises.push(fetchJSON(pubchemURL));
-    }
-  }
-
-  let results = await Promise.all(promises);
-
-  let mfs = [];
-  for (let i = 0; i < results.length; i++) {
-    for (const entry of results[i].data) {
-      if (
-        allowedEMs &&
-        !allowedEMs.find((em) => Math.abs(em - entry.em) < 0.0000001)
-      ) {
-        continue;
-      }
-      try {
-        let mfInfo = new mfParser.MF(entry._id).getInfo();
-        mfInfo.ionization = ionizations[i];
-        mfInfo.em = mfInfo.monoisotopicMass;
-        mfInfo.ms = mfUtilities.getMsInfo(mfInfo, {
-          targetMass: masses,
-        }).ms;
-        mfInfo.info = { nbPubchemEntries: entry.count };
-        mfs.push(mfInfo);
-      } catch (e) {
-        // eslint-disable-next-line no-console
-        console.warn(`${e}`);
-      }
-    }
-  }
-  // because we can combine many ionizations we should resort the data
-  mfs.sort((a, b) => Math.abs(a.ms.ppm) - Math.abs(b.ms.ppm));
-  return mfs;
-}
-
-/**
- * Generates a database 'pubchem' based on all molecular formula available
- * in the database and a monoisotopic mass.
- * @param {number|string|number[]} masses - Observed monoisotopic mass
- * @param {object} [options={}]
- * @param {string} [options.databaseName='pubchem']
- * @param {string} [options.ionizations=''] - string containing a comma separated list of modifications
- * @param {string} [options.ranges=''] -
- * @param {number} [options.precision=1000] - Precision of the monoisotopic mass in ppm
- * @param {number} [options.limit=1000] - Maximal number of entries to return
- * @param {string} [options.url='https://pubchem.cheminfo.org/activesOrNaturals/v1/fromEM'] - URL of the webservice
- */
-
-async function searchActivesOrNaturals(masses, options = {}) {
-  const {
-    url = 'https://pubchem.cheminfo.org/activesOrNaturals/v1/fromEM',
-    precision = 1000,
-    limit = 1000,
-    ranges = '',
-  } = options;
-
-  if (typeof masses === 'number') {
-    masses = [masses];
-  }
-  if (typeof masses === 'string') {
-    masses = masses.split(/[\r\n\t,; ]+/).map(Number);
-  }
-  let promises = [];
-  let ionizations = mfUtilities.preprocessIonizations(options.ionizations);
-
-  let allowedEMs; // we prefer to use the exact mass rather than MF
-  if (ranges) {
-    const allowedEMsArray = [];
-    for (let mass of masses) {
-      (
-        await mfFinder.findMFs(mass, {
-          ionizations: options.ionizations,
-          precision,
-          ranges,
-          limit: 100000,
-        })
-      ).mfs.forEach((mf) => allowedEMsArray.push(mf.em));
-    }
-    allowedEMs = Float64Array.from(allowedEMsArray).sort();
-  }
-
-  for (let mass of masses) {
-    for (let ionization of ionizations) {
-      let realMass =
-        mass * Math.abs(ionization.charge || 1) -
-        ionization.em +
-        chemicalElements.ELECTRON_MASS * ionization.charge;
-
-      const pubchemURL = `${url}?em=${realMass}&precision=${precision}&limit=${limit}`;
-      promises.push(fetchJSON(pubchemURL));
-    }
-  }
-
-  let results = await Promise.all(promises);
-  let mfs = [];
-  for (let i = 0; i < results.length; i++) {
-    for (let mf of results[i].data) {
-      try {
-        // would it be more efficient to filter later ???
-        if (
-          allowedEMs &&
-          !allowedEMs.find((em) => Math.abs(em - mf.data.em) < 0.0000001)
-        ) {
-          continue;
-        }
-
-        let mfInfo = new mfParser.MF(mf.data.mf).getInfo();
-        mfInfo.ionization = ionizations[i];
-        mfInfo.em = mfInfo.monoisotopicMass;
-        mfInfo.ms = mfUtilities.getMsInfo(mfInfo, {
-          targetMass: masses,
-        }).ms;
-
-        const info = mf.data;
-        info.idCode = mf.id;
-
-        delete info.em;
-        delete info.charge;
-        delete info.unsaturation;
-        delete info.mf;
-
-        mfInfo.info = mf.data;
-        mfs.push(mfInfo);
-      } catch (e) {
-        // eslint-disable-next-line no-console
-        console.warn(`${e}`);
-      }
-    }
-  }
-
-  // we will now group the data per mf
-  const grouped = {};
-  for (const mf of mfs) {
-    if (!grouped[mf.mf]) {
-      grouped[mf.mf] = {
-        mf: mf.mf,
-        em: mf.em,
-        ms: mf.ms,
-        molecules: [],
-        nbNatural: 0,
-        nbBioactive: 0,
-        nbPubmed: 0,
-        nbWithMassSpectra: 0,
-      };
-    }
-    grouped[mf.mf].molecules.push(mf);
-
-    if (mf.info.naturalProduct) grouped[mf.mf].nbNatural++;
-    if (mf.info.bioActive) grouped[mf.mf].nbBioactive++;
-    if (mf.info.nbMassSpectra) grouped[mf.mf].nbWithMassSpectra++;
-    if (mf.info.pubmeds && mf.info.pubmeds.length > 0) {
-      grouped[mf.mf].nbPubmed++;
-    }
-  }
-
-  const groupedArray = Object.keys(grouped).map((key) => grouped[key]);
-  // because we can combine many ionizations we should resort the data
-  groupedArray.sort((a, b) => Math.abs(a.ms.ppm) - Math.abs(b.ms.ppm));
-
-  return groupedArray;
-}
-
-/**
  * Calculates a function that allows post-calibration on mass spectra based on the error in assignment
@@ -1327,2 +1105,7 @@ * @param {*} similarities
 
+async function fetchJSON(url) {
+  const result = await crossFetch__default["default"](url);
+  return result.json();
+}
+
 /**
@@ -1507,3 +1290,1 @@ * A class that deals with database of monoisotopic mass and molecular formula
 exports.massShifts = massShifts;
-exports.searchActivesOrNaturals = searchActivesOrNaturals;
-exports.searchPubchem = searchPubchem;

package.json

 {
   "name": "emdb",
-  "version": "2.3.0",
+  "version": "2.4.0",
   "description": "Database manager for exact mass query",
@@ -26,15 +26,15 @@ "main": "lib/index.js",
     "cross-fetch": "^3.1.5",
-    "isotopic-distribution": "^2.1.0",
+    "isotopic-distribution": "^2.2.0",
     "jszip": "^3.10.1",
-    "mass-fragmentation": "^0.2.5",
-    "mf-finder": "^2.3.0",
-    "mf-from-google-sheet": "^2.0.6",
-    "mf-generator": "^2.1.0",
+    "mass-fragmentation": "^0.3.0",
+    "mf-finder": "^2.4.0",
+    "mf-from-google-sheet": "^2.0.7",
+    "mf-generator": "^2.1.1",
     "mf-matcher": "^2.1.0",
-    "mf-parser": "^2.2.1",
-    "mf-utilities": "^2.0.3",
+    "mf-parser": "^2.3.0",
+    "mf-utilities": "^2.0.4",
     "ml-regression-theil-sen": "^2.0.0",
     "ml-spectra-processing": "^12.0.0",
-    "ms-spectrum": "^2.3.2",
-    "nucleotide": "^2.0.3",
+    "ms-spectrum": "^2.4.0",
+    "nucleotide": "^2.1.0",
     "openchemlib-utils": "^2.4.0",
@@ -49,3 +49,3 @@ "peaks-similarity": "^3.1.1",
   },
-  "gitHead": "d309de1c7a86730c8e4f0bd836896e1a16c95cb7"
+  "gitHead": "2f92cd4423018e7dad9594565f1fae4557de0ca3"
 }

src/__tests__/loadKnapSack.test.js

 import { loadKnapSack } from '../loadKnapSack';
 
-jest.setTimeout(30000);
 test('loadKnapSack', async () => {
@@ -5,0 +4,0 @@ let data = await loadKnapSack();

src/__tests__/search.test.js

 import { EMDB } from '..';
 
-jest.setTimeout(30000);
-
 describe('test search', () => {
@@ -6,0 +4,0 @@ it('should filter one database', async () => {

src/__tests__/searchCommercials.test.js

 import { EMDB } from '..';
 
-jest.setTimeout(30000);
-
 describe('test search commercial', () => {
@@ -6,0 +4,0 @@ it('should filter the commercial database', async () => {

src/__tests__/searchMSEM.test.js

 import { EMDB } from '..';
 
-jest.setTimeout(20000);
-
 describe('test searchMSEM', () => {
@@ -6,0 +4,0 @@ it('should filter one database with existing ionization', async () => {

src/index.js

@@ -17,4 +17,2 @@ import { Spectrum } from 'ms-spectrum';
 
-export * from './searchPubchem.js';
-export * from './searchActivesOrNaturals.js';
 export * from './massShifts.js';
@@ -21,0 +19,0 @@ export * from './util/fetchJSON.js';

No alert changes

Worsened metrics

Total package byte prevSize

1325461

decreased by-1.57%

Number of package files

49

decreased by-9.26%

Lines of code

3415

decreased by-12.37%

Dependency changes

• + Addedmass-fragmentation@0.3.0(transitive)

• - Removedmass-fragmentation@0.2.5(transitive)

• Updatedisotopic-distribution@^2.2.0

• Updatedmass-fragmentation@^0.3.0

• Updatedmf-finder@^2.4.0

• Updatedmf-from-google-sheet@^2.0.7

• Updatedmf-generator@^2.1.1

• Updatedmf-parser@^2.3.0

• Updatedmf-utilities@^2.0.4

• Updatedms-spectrum@^2.4.0

• Updatednucleotide@^2.1.0