chore: handle many eslint errors

.github/workflows/nodejs.yml

@@ -26,4 +26,4 @@ jobs:
       - name: Install dependencies
         run: npm ci
       - name: Run babel on all files
-        run: npm run babel
+        run: npm run babel-test

ChemEquilibrium/AcidModel.js

@@ -147,7 +147,7 @@ let pkas = [
   { ha: 'HCl', a: 'Cl-', pka: 1, specie: { label: 'Cl-', number: 1, pka: 1 } },
 ];
 
-define(['lodash'], function (_) {
+define(['lodash'], (_) => {
   class AcidBase {
     constructor(customPkas) {
       this.pkas = customPkas || pkas;
@@ -165,14 +165,14 @@ define(['lodash'], function (_) {
 
     addAcidBase(label, total) {
       let titrProtonCount;
-      let titrSpecie = pkas.find(function (pka) {
+      let titrSpecie = pkas.find(function equalsLabel(pka) {
         return pka.ha === label;
       });
       if (titrSpecie) {
         titrProtonCount = titrSpecie.specie.number;
         titrSpecie = titrSpecie.specie.label;
       } else {
-        titrSpecie = pkas.find(function (pka) {
+        titrSpecie = pkas.find(function equalsLabel(pka) {
           return pka.a === label;
         });
         if (titrSpecie) {
@@ -222,13 +222,13 @@ define(['lodash'], function (_) {
     getModel() {
       // Get all involved pkas
       let pkas = this.pkas.filter((pka) => {
-        return this.components.find(function (c) {
+        return this.components.find(function equalsLabel(c) {
           return String(c.label) === String(pka.specie.label);
         });
       });
 
       // group pkas by component
-      let grouped = _.groupBy(pkas, function (pka) {
+      let grouped = _.groupBy(pkas, function equalsLabel(pka) {
         return String(pka.specie.label);
       });
 
@@ -241,7 +241,7 @@ define(['lodash'], function (_) {
 
       // Model components
       model.components = new Array(nbComponents);
-      for (i = 0; i < this.components.length; i++) {
+      for (let i = 0; i < this.components.length; i++) {
         model.components[i] = { ...this.components[i] };
       }
 
@@ -256,7 +256,7 @@ define(['lodash'], function (_) {
 
       model.formedSpecies[0].components[protonIndex] = -1;
 
-      for (var i = 0; i < this.components.length; i++) {
+      for (let i = 0; i < this.components.length; i++) {
         if (i === protonIndex) continue;
         let group = grouped[this.components[i].label];
         if (!group) throw new Error('Should be unreachable');

ChemEquilibrium/chart.js

@@ -1,4 +1,4 @@
-define(['src/util/color'], function (Color) {
+define(['src/util/color'], (Color) => {
   return {
     getChart(x, y, options) {
       options = options || {};
@@ -20,10 +20,9 @@ define(['src/util/color'], function (Color) {
       let species = Object.keys(y[0]);
       let colors = Color.getDistinctColors(species.length);
 
-      for (var i = 0; i < species.length; i++) {
+      for (let i = 0; i < species.length; i++) {
         let data = {};
         chart.data.push(data);
-        // eslint-disable-next-line no-loop-func
         data.y = y.map((y) => {
           return y[species[i]];
         });

biology/needleman/index.js

@@ -49,7 +49,7 @@ function run(v, w, options = {}) {
       let matrixScore;
       try {
         matrixScore = S[v[i - 1]][w[j - 1]];
-      } catch (e) {
+      } catch {
         // e.g. a letter is not found in the matrix
         matrixScore = indel;
       }

chemistry/PubChem.js

@@ -10,7 +10,6 @@ async function getMolecules(mf) {
 
   let response = await fetch(`${pubchemURL}${searchParams.toString()}`);
   let results = await response.json();
-  console.log(results.data);
   return results.data;
 }
 
@@ -66,7 +65,7 @@ module.exports = {
           rowHeight: 140,
         },
       })
-      .catch(function (e) {
+      .catch((e) => {
         console.error(e); // eslint-disable-line no-console
         ui.showNotification('search failed', 'error');
       });

chemistry/chemcalcSequenceSVG.js

@@ -1,7 +1,7 @@
 define([
   'https://www.lactame.com/github/adobe-webplatform/Snap.svg/84fbff7d512c8145c522b71fc9c872cb0bcae49a/dist/snap.svg-min.js',
   './sequenceSplitter',
-], function (Snap, sequenceSplitter) {
+], (snap, sequenceSplitter) => {
   function getSVG(sequence, analysisResult, options) {
     const {
       width = 600,
@@ -24,7 +24,7 @@ define([
 
     let line = 0;
     // we create a temporary paper in order to get the width of the text blocs
-    let tempPaper = Snap(1000, 40);
+    let tempPaper = snap(1000, 40);
     for (let i = 0; i < mfParts.length; i++) {
       let part = mfParts[i];
       let text = tempPaper.text(xPos, 20, part);
@@ -130,11 +130,11 @@ define([
       rowHeight * (line + 1) + 50 + verticalShiftForTerminalAnnotations;
 
     // We start to create the SVG and create the paper
-    let paper = Snap(width, height);
+    let paper = snap(width, height);
 
     addScript(paper);
 
-    residues.forEach(function (residue) {
+    residues.forEach((residue) => {
       residue.y = (residue.line + 1) * rowHeight;
       let text = paper.text(residue.xFrom, residue.y, residue.label);
       text.attr({ id: `residue-${residue.nTer}` });
@@ -163,7 +163,7 @@ define([
       let used = {};
       for (let i = from; i < to; i++) {
         let residue = residues[i];
-        residue.usedSlots.forEach(function (usedSlot, index) {
+        residue.usedSlots.forEach((usedSlot, index) => {
           used[index] = true;
         });
       }
@@ -182,7 +182,7 @@ define([
 
     function drawTerminals() {
       for (let result of results) {
-        var residue;
+        let residue;
         let nTerminal = false;
         if (result.fromNTerm) {
           residue = residues[result.to];
@@ -267,7 +267,7 @@ define([
           // var charge = result.charge > 0 ? '+' + result.charge : result.charge;
           // var label = result.type + ' (' + charge + ', ' + Math.round(result.similarity) + '%)';
           // we need to check on how many lines we are
-          var fromX, toX, y;
+          let fromX, toX, y;
           for (let line = fromResidue.line; line <= toResidue.line; line++) {
             y =
               -10 -

chemistry/orbitals.js

@@ -1,6 +1,6 @@
 define([
   'https://www.lactame.com/github/adobe-webplatform/Snap.svg/84fbff7d512c8145c522b71fc9c872cb0bcae49a/dist/snap.svg-min.js',
-], function (Snap) {
+], (snap) => {
   let exports = {};
 
   let defaultOptions = {
@@ -133,7 +133,7 @@ define([
     }
 
     svgModifier = [];
-    paper = Snap(width, height);
+    paper = snap(width, height);
 
     paper
       .path('M 0 0 L 10 4 L 0 8 z')
@@ -216,7 +216,7 @@ define([
 
   function parseelConfig(elConfig) {
     elConfig = elConfig.split(' ');
-    elConfig = elConfig.map(function (o) {
+    elConfig = elConfig.map((o) => {
       let m = o.match(/^(\d\w)(\d+)/);
       return {
         layer: m[1],
@@ -282,11 +282,11 @@ define([
     return Math.floor(electron / num) === 0 ? 1 : -1;
   }
 
-  exports.getSvg = function (...args) {
+  exports.getSvg = function getSvg(...args) {
     createSvg(args);
     return svg;
   };
-  exports.getSvgAndModifier = function (...args) {
+  exports.getSvgAndModifier = function getSvgAndModifier(...args) {
     createSvg(args);
     return { svg, svgModifier };
   };

chemistry/structuralAnalysisExercises.js

@@ -43,9 +43,9 @@
     }
     let datum = data[file.rn];
     switch (file.kind) {
-      case 'mol':
+      case 'mol': {
         datum.mol = { type: 'mol2d', url: file.url };
         const molfile = await (await fetch(file.url)).text();
         const molecule = Molecule.fromMolfile(molfile);
         datum.oclCode = molecule.getIDCode();
         datum.id = datum.rn;
@@ -61,6 +61,7 @@
         datum.nbH = Number(datum.mf.replace(/.*H([0-9]+).*/, '$1'));
         datum.nbC = Number(datum.mf.replace(/.*C([0-9]+).*/, '$1'));
         break;
+      }
       case 'mass':
         datum.mass = { type: 'jcamp', url: file.url };
         datum.isMass = true;

defaultOptions/mass.js

@@ -1,4 +1,4 @@
-define(function () {
+define(() => {
   return {
     monoisotopicMass: 300.123,
     resolution: 100000,

edx/channel.js

@@ -1,6 +1,6 @@
 define([
   'https://cdnjs.cloudflare.com/ajax/libs/jschannel/1.0.0-git-commit1-8c4f7eb/jschannel.js',
-], function () {
+], () => {
   let initialized = false;
   function init(options) {
     if (initialized) return;

eln/BioReaction.js

@@ -177,10 +177,11 @@
       case 'save':
         await this.roc.update(this.sample);
         break;
-      case 'deleteAttachment':
-        var attachment = action.value.name;
+      case 'deleteAttachment': {
+        const attachment = action.value.name;
         await this.roc.deleteAttachment(this.sample, attachment);
         break;
+      }
       case 'unattach':
         await this.roc.unattach(this.sample, action.value);
         break;
@@ -217,7 +218,7 @@
     }
     for (let i = 0; i < files.length; i++) {
       const data = DataObject.resurrect(files[i]);
       await this.roc.attach(type, this.sample, data);
     }
   }
 }

eln/ExpandableMolecule.js

@@ -208,10 +208,11 @@ class ExpandableMolecule {
       case 'toggleJSMEEdition':
         this.toggleJSMEEdition(!this.jsmeEditionMode);
         break;
-      case 'clearMolfile':
-        var molfile = API.getData('editableMolfile');
+      case 'clearMolfile': {
+        const molfile = API.getData('editableMolfile');
         molfile.setValue('');
         break;
+      }
       case 'swapHydrogens':
         this.setExpandedHydrogens();
         break;

eln/ExtSample.js

@@ -100,7 +100,7 @@
         case '$content.general.mf':
           try {
             this.mf.fromMF();
-          } catch (e) {
+          } catch {
             // ignore
           }
           break;
@@ -119,7 +119,7 @@
   }
 
   async _init() {
-    this._initialized = new Promise(async (resolve) => {
+    this._initialized = (async () => {
       let sample;
       if (this.options.trackId) {
         try {
@@ -143,8 +143,7 @@
         sample.$content.general.molfile = ''; // can not be edited otherwise
       }
       this._loadSample(sample);
-      resolve();
-    });
+    })();
   }
 
   bindChange() {
@@ -157,7 +156,7 @@
   }
 
   async handleDrop(name, askType, options = {}) {
-    let { converters = {}, autoJcamp, autoKind } = options;
+    let { converters = {}, autoKind } = options;
     if (!name) {
       throw new Error('handleDrop expects a variable name');
     }
@@ -201,15 +200,13 @@
       }
 
       if (converters[kind]) {
-        autoJcamp = false;
-
         let converted = await converters[kind](droppedData.content);
         if (!Array.isArray(converted)) {
           converted = [converted];
         }
 
         for (let i = 1; i < converted.length; i++) {
           newData.push({
             filename: droppedData.filename.replace(/\.[^.]*$/, `_${i}.jdx`),
             mimetype: 'chemical/x-jcamp-dx',
             contentType: 'chemical/x-jcamp-dx',

eln/MF.js

@@ -20,9 +20,9 @@ class MF {
           let mfInfo = new MolecularFormula.MF(mf).getInfo();
           this.setCanonizedMF(mfInfo.mf);
           this.previousEMMF = mfInfo.monoisotopicMass;
-        } catch (e) {
+        } catch (err) {
           this.setCanonizedMF('');
-          console.log('Could not parse MF: ', mf);
+          reportError(err);
         }
       }
     }
@@ -97,10 +97,6 @@ class MF {
     this.sample.setChildSync(['$content', 'general', 'mf'], mf);
   }
 
-  setMF(mf) {
-    this.sample.setChildSync(['$content', 'general', 'mf'], mf);
-  }
-
   setMW(mw) {
     this.sample.setChildSync(['$content', 'general', 'mw'], mw);
   }

eln/Nmr1dManager.js

@@ -177,13 +177,14 @@
         this._autoRanges(currentNmr);
         break;
       }
-      case 'deleteAllRanges':
-        var ranges = API.getData('currentNmrRanges');
+      case 'deleteAllRanges': {
+        const ranges = API.getData('currentNmrRanges');
         while (ranges.length) {
           ranges.pop();
         }
         ranges.triggerChange();
         break;
+      }
       case 'clearAssignments': {
         let ranges = this.getCurrentRanges();
         if (ranges) {
@@ -298,8 +299,9 @@
   _getNMR(currentNMRLine) {
     let filename = String(currentNMRLine.getChildSync(['jcamp', 'filename']));
     return currentNMRLine.getChild(['jcamp', 'data']).then((jcamp) => {
+      let spectrum;
       if (filename && this.spectra[filename]) {
-        var spectrum = this.spectra[filename];
+        spectrum = this.spectra[filename];
       } else if (jcamp) {
         jcamp = String(jcamp.get());
         spectrum = NMR.fromJcamp(jcamp);
@@ -381,7 +383,7 @@
         if (mfInfo && mfInfo.atoms && mfInfo.atoms.H) {
           return mfInfo.atoms.H || 100;
         }
-      } catch (e) {
+      } catch {
         return 100;
       }
     }
@@ -397,7 +399,7 @@
     }
   }
 
   // todo : migrate this code to spectra-data-ranges
   getRangesTotalIntegral() {
     let ranges = API.getData('currentNmrRanges') || [];
     let sum = 0;