emdb - npm Package Compare versions

Comparing version 0.6.4 to 0.7.0

package.json

 {
   "name": "emdb",
-  "version": "0.6.4",
+  "version": "0.7.0",
   "description": "Database manager for exact mass query",
@@ -25,11 +25,11 @@ "browser": {
   "dependencies": {
-    "isotopic-distribution": "^0.6.4",
+    "isotopic-distribution": "^0.7.0",
     "jszip": "^3.1.5",
-    "mf-finder": "^0.6.4",
-    "mf-from-google-sheet": "^0.6.4",
-    "mf-generator": "^0.6.4",
-    "mf-matcher": "^0.6.4",
-    "mf-parser": "^0.6.4",
-    "mf-utilities": "^0.6.4",
-    "nucleotide": "^0.6.4",
+    "mf-finder": "^0.7.0",
+    "mf-from-google-sheet": "^0.7.0",
+    "mf-generator": "^0.7.0",
+    "mf-matcher": "^0.7.0",
+    "mf-parser": "^0.7.0",
+    "mf-utilities": "^0.7.0",
+    "nucleotide": "^0.7.0",
     "peaks-similarity": "^2.3.0",
@@ -36,0 +36,0 @@ "peptide": "^1.6.1",

src/__tests__/DBManager.js

@@ -5,4 +5,2 @@ 'use strict';
 
-jest.setTimeout(30000);
-
 test('test DBManager contaminants and knapSack', async () => {
@@ -16,3 +14,3 @@ let dbManager = new DBManager();
   expect(dbManager.get('contaminants').length).toBeGreaterThan(1000);
-});
+}, 30000);
 
@@ -22,5 +20,3 @@ test('test DBManager fromMonoisotopicMass', () => {
 
-  dbManager.fromMonoisotopicMass(300, {
-    ionizations: 'H+,Na+'
-  });
+  dbManager.fromMonoisotopicMass(300, { ionizations: 'H+,Na+' });
 
@@ -27,0 +23,0 @@ expect(dbManager.listDatabases()).toEqual(['monoisotopic']);

src/__tests__/loadGoogleSheet.js

@@ -5,13 +5,13 @@ 'use strict';
 
+
 test('test load google sheet', async () => {
+  let data = await loadGoogleSheet();
+  expect(data.length).toBeGreaterThan(1000);
 
-    let data = await loadGoogleSheet();
-    expect(data.length).toBeGreaterThan(1000);
-
-    let first = data[0];
-    expect(first.mf).toBe('CN');
-    expect(first.ionization).toEqual({ charge: -1, em: 0, mf: '(-)' });
-    expect(first.em).toBeGreaterThan(0);
-    expect(first.ms.charge).not.toBe(0);
-    expect(first.ms.em).toBeGreaterThan(0);
-});
+  let first = data[0];
+  expect(first.mf).toBe('CN');
+  expect(first.ionization).toEqual({charge: -1, em: 0, mf: '(-)'});
+  expect(first.em).toBeGreaterThan(0);
+  expect(first.ms.charge).not.toBe(0);
+  expect(first.ms.em).toBeGreaterThan(0);
+}, 10000);

src/searchPubchem.js

@@ -17,44 +17,40 @@ 'use strict';
  * @param {number} [options.allowNeutralMolecules=false] - Should we display uncharged molecules (non observable by mass)
- * @param {number} [options.url='https://pubchem2.cheminfo.org/mfs/em'] - URL of the webservice
+ * @param {number} [options.url='https://pubchem.cheminfo.org/mfs/em'] - URL of the webservice
  */
 
 module.exports = async function searchPubchem(mass, options = {}) {
-    const {
-        url = 'https://pubchem2.cheminfo.org/mfs/em',
-        precision = 1000,
-        allowNeutralMolecules = false
-    } = options;
+  const {
+    url = 'https://pubchem.cheminfo.org/mfs/em',
+    precision = 1000,
+    allowNeutralMolecules = false
+  } = options;
 
-    let promises = [];
-    let ionizations = preprocessIonizations(options.ionizations);
-    for (let ionization of ionizations) {
-        let realMass = mass * ionization.charge - ionization.em;
-        promises.push(fetch(`${url}?em=${realMass}&precision=${precision}`));
-    }
+  let promises = [];
+  let ionizations = preprocessIonizations(options.ionizations);
+  for (let ionization of ionizations) {
+    let realMass = mass * ionization.charge - ionization.em;
+    promises.push(fetch(`${url}?em=${realMass}&precision=${precision}`));
+  }
 
-    let results = await Promise.all(promises);
+  let results = await Promise.all(promises);
 
-    let mfs = [];
-    for (let i = 0; i < results.length; i++) {
-        for (let mf of results[i].result) {
-            try {
-                let mfInfo = new mfParser.MF(mf.mf).getInfo();
-                mfInfo.ionization = ionizations[i];
-                mfInfo.em = mfInfo.monoisotopicMass;
-                mfInfo.ms = getMsInfo(mfInfo, {
-                    targetMass: mass,
-                    allowNeutralMolecules
-                });
-                mfInfo.info = {
-                    nbPubchemEntries: mf.total
-                };
-                mfs.push(mfInfo);
-            } catch (e) {
-                console.warn(`${e}`);
-            }
-        }
+  let mfs = [];
+  for (let i = 0; i < results.length; i++) {
+    for (let mf of results[i].result) {
+      try {
+        let mfInfo = new mfParser.MF(mf.mf).getInfo();
+        mfInfo.ionization = ionizations[i];
+        mfInfo.em = mfInfo.monoisotopicMass;
+        mfInfo.ms =
+            getMsInfo(mfInfo, {targetMass: mass, allowNeutralMolecules});
+        mfInfo.info = {nbPubchemEntries: mf.total};
+        mfs.push(mfInfo);
+      } catch (e) {
+        console.warn(`${e}`);
+      }
     }
-    // because we can combine many ionizations we should resort the data
-    mfs.sort((a, b) => a.ms.ppm - b.ms.ppm);
-    return mfs;
+  }
+  // because we can combine many ionizations we should resort the data
+  mfs.sort((a, b) => a.ms.ppm - b.ms.ppm);
+  return mfs;
 };

No alert changes

Worsened metrics

Total package byte prevSize

97365

decreased by-3.31%

Lines of code

1010

decreased by-0.69%

Dependency changes

• + Addedatom-sorter@0.7.0(transitive)

• + Addedchemical-elements@0.7.0(transitive)

• + Addedchemical-groups@0.7.0(transitive)

• + Addedisotopic-distribution@0.7.0(transitive)

• + Addedmf-finder@0.7.0(transitive)

• + Addedmf-from-google-sheet@0.7.0(transitive)

• + Addedmf-generator@0.7.0(transitive)

• + Addedmf-matcher@0.7.0(transitive)

• + Addedmf-parser@0.7.0(transitive)

• + Addedmf-utilities@0.7.0(transitive)

• + Addednucleotide@0.7.0(transitive)

• - Removedatom-sorter@0.6.4(transitive)

• - Removedchemical-elements@0.6.4(transitive)

• - Removedchemical-groups@0.6.4(transitive)

• - Removedisotopic-distribution@0.6.4(transitive)

• - Removedmf-finder@0.6.4(transitive)

• - Removedmf-from-google-sheet@0.6.4(transitive)

• - Removedmf-generator@0.6.4(transitive)

• - Removedmf-matcher@0.6.4(transitive)

• - Removedmf-parser@0.6.4(transitive)

• - Removedmf-utilities@0.6.4(transitive)

• - Removednucleotide@0.6.4(transitive)

• Updatedisotopic-distribution@^0.7.0

• Updatedmf-finder@^0.7.0

• Updatedmf-from-google-sheet@^0.7.0

• Updatedmf-generator@^0.7.0

• Updatedmf-matcher@^0.7.0

• Updatedmf-parser@^0.7.0

• Updatedmf-utilities@^0.7.0

• Updatednucleotide@^0.7.0