diff --git a/.babelrc b/.babelrc
deleted file mode 100644
index 1320b9a3..00000000
--- a/.babelrc
+++ /dev/null
@@ -1,3 +0,0 @@
-{
- "presets": ["@babel/preset-env"]
-}
diff --git a/.github/workflows/nodejs.yml b/.github/workflows/nodejs.yml
index 1ab1e710..d6267d73 100644
--- a/.github/workflows/nodejs.yml
+++ b/.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
diff --git a/ChemEquilibrium/AcidModel.js b/ChemEquilibrium/AcidModel.js
index ad7d48c9..43fdb8a3 100644
--- a/ChemEquilibrium/AcidModel.js
+++ b/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');
diff --git a/ChemEquilibrium/chart.js b/ChemEquilibrium/chart.js
index 816251c3..1d400209 100644
--- a/ChemEquilibrium/chart.js
+++ b/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]];
});
diff --git a/biology/needleman/index.js b/biology/needleman/index.js
index 3d414eb4..ab98d91b 100644
--- a/biology/needleman/index.js
+++ b/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;
}
diff --git a/chemistry/PubChem.js b/chemistry/PubChem.js
index 203bfc00..12af9427 100644
--- a/chemistry/PubChem.js
+++ b/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');
});
diff --git a/chemistry/chemcalcSequenceSVG.js b/chemistry/chemcalcSequenceSVG.js
index 16d33692..55abcfaf 100644
--- a/chemistry/chemcalcSequenceSVG.js
+++ b/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 -
diff --git a/chemistry/orbitals.js b/chemistry/orbitals.js
index 375def68..fec4c1ac 100644
--- a/chemistry/orbitals.js
+++ b/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 };
};
diff --git a/chemistry/structuralAnalysisExercises.js b/chemistry/structuralAnalysisExercises.js
index c9b04bbf..798563bd 100644
--- a/chemistry/structuralAnalysisExercises.js
+++ b/chemistry/structuralAnalysisExercises.js
@@ -43,7 +43,7 @@ async function fetchData(
}
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);
@@ -61,6 +61,7 @@ async function fetchData(
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;
diff --git a/defaultOptions/mass.js b/defaultOptions/mass.js
index 6e440873..e83a9800 100644
--- a/defaultOptions/mass.js
+++ b/defaultOptions/mass.js
@@ -1,4 +1,4 @@
-define(function () {
+define(() => {
return {
monoisotopicMass: 300.123,
resolution: 100000,
diff --git a/edx/channel.js b/edx/channel.js
index d7fc7f6f..e28051da 100644
--- a/edx/channel.js
+++ b/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;
diff --git a/eln/.eslintrc.yml b/eln/.eslintrc.yml
deleted file mode 100644
index add5a785..00000000
--- a/eln/.eslintrc.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-parserOptions:
- sourceType: module
diff --git a/eln/BioReaction.js b/eln/BioReaction.js
index ee4eea36..80f6daab 100644
--- a/eln/BioReaction.js
+++ b/eln/BioReaction.js
@@ -177,10 +177,11 @@ class BioReaction {
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;
diff --git a/eln/ExpandableMolecule.js b/eln/ExpandableMolecule.js
index 6994a125..fa1a7498 100644
--- a/eln/ExpandableMolecule.js
+++ b/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;
diff --git a/eln/ExtSample.js b/eln/ExtSample.js
index 7430f2a8..636daf1e 100644
--- a/eln/ExtSample.js
+++ b/eln/ExtSample.js
@@ -100,7 +100,7 @@ class Sample {
case '$content.general.mf':
try {
this.mf.fromMF();
- } catch (e) {
+ } catch {
// ignore
}
break;
@@ -119,7 +119,7 @@ class Sample {
}
async _init() {
- this._initialized = new Promise(async (resolve) => {
+ this._initialized = (async () => {
let sample;
if (this.options.trackId) {
try {
@@ -143,8 +143,7 @@ class Sample {
sample.$content.general.molfile = ''; // can not be edited otherwise
}
this._loadSample(sample);
- resolve();
- });
+ })();
}
bindChange() {
@@ -157,7 +156,7 @@ class Sample {
}
async handleDrop(name, askType, options = {}) {
- let { converters = {}, autoJcamp, autoKind } = options;
+ let { converters = {}, autoKind } = options;
if (!name) {
throw new Error('handleDrop expects a variable name');
}
@@ -201,8 +200,6 @@ class Sample {
}
if (converters[kind]) {
- autoJcamp = false;
-
let converted = await converters[kind](droppedData.content);
if (!Array.isArray(converted)) {
converted = [converted];
diff --git a/eln/MF.js b/eln/MF.js
index a69d96ca..b8e27ca0 100644
--- a/eln/MF.js
+++ b/eln/MF.js
@@ -20,9 +20,9 @@ class MF {
let mfInfo = new MolecularFormula.MF(mf).getInfo();
this.setCanonizedMF(mfInfo.mf);
this.previousEMMF = mfInfo.monoisotopicMass;
- } catch (e) {
+ } catch (err) {
this.setCanonizedMF('');
- console.log('Could not parse MF: ', mf);
+ reportError(err);
}
}
}
@@ -97,10 +97,6 @@ class MF {
this.sample.setChildSync(['$content', 'general', 'mf'], mf);
}
- setMF(mf) {
- this.sample.setChildSync(['$content', 'general', 'mf'], mf);
- }
-
setMW(mw) {
this.sample.setChildSync(['$content', 'general', 'mw'], mw);
}
diff --git a/eln/Nmr1dManager.js b/eln/Nmr1dManager.js
index 5e7f54aa..dd134d42 100644
--- a/eln/Nmr1dManager.js
+++ b/eln/Nmr1dManager.js
@@ -177,13 +177,14 @@ class Nmr1dManager {
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 @@ class Nmr1dManager {
_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 @@ class Nmr1dManager {
if (mfInfo && mfInfo.atoms && mfInfo.atoms.H) {
return mfInfo.atoms.H || 100;
}
- } catch (e) {
+ } catch {
return 100;
}
}
diff --git a/eln/Sample.js b/eln/Sample.js
index 25f3d871..4ffb765f 100644
--- a/eln/Sample.js
+++ b/eln/Sample.js
@@ -616,11 +616,15 @@ Your local changes will be lost.`;
content = atob(droppedData.content);
droppedData.encoding = 'text';
break;
- case 'buffer':
+ case 'buffer': {
const decoder = new TextDecoder();
content = decoder.decode(droppedData.content);
droppedData.encoding = 'text';
break;
+ }
+ default: {
+ // No special handling
+ }
}
droppedData.content = convertToJcamp(content, {
meta,
@@ -675,8 +679,8 @@ Your local changes will be lost.`;
case 'translateNucleic':
Sequence.translateNucleic(this.sample);
break;
- case 'createOptions':
- var advancedOptions1H = API.cache('nmr1hAdvancedOptions');
+ case 'createOptions': {
+ const advancedOptions1H = API.cache('nmr1hAdvancedOptions');
if (advancedOptions1H) {
API.createData(
'nmr1hOndeTemplate',
@@ -689,9 +693,11 @@ Your local changes will be lost.`;
);
}
break;
+ }
case 'recreateVariables':
this.createVariables();
- case 'deleteAttachment':
+ break;
+ case 'deleteAttachment': {
const ok = await UI.confirm(
'Are you sure you want to delete the attachment?',
);
@@ -700,6 +706,7 @@ Your local changes will be lost.`;
await this.roc.deleteAttachment(this.sample, attachment);
this.updateOtherAttachments();
break;
+ }
case 'deleteNmr': // Deprecated. Use unattach. Leave this for backward compatibility
case 'unattach':
if (
@@ -845,7 +852,6 @@ async function pasteAnalysis(sample) {
API.doAction('refresh', { noConfirmation: true });
function getName(existingAttachments, filename) {
- console.log({ existingAttachments, filename });
if (!existingAttachments[filename]) {
return filename;
}
diff --git a/eln/StockSample.js b/eln/StockSample.js
index 86568a17..007fd52f 100644
--- a/eln/StockSample.js
+++ b/eln/StockSample.js
@@ -56,7 +56,7 @@ class Sample {
case '$content.general.mf':
try {
this.mf.fromMF();
- } catch (e) {
+ } catch {
// ignore
}
break;
@@ -69,11 +69,10 @@ class Sample {
}
async _init() {
- this._initialized = new Promise(async (resolve) => {
+ this._initialized = (async () => {
this.sample = await API.createData(this.options.varName, this.sample);
this._loadSample();
- resolve();
- });
+ })();
}
bindChange() {
diff --git a/eln/nucleic/genbank.js b/eln/nucleic/genbank.js
index 0f0a79ee..4080f010 100644
--- a/eln/nucleic/genbank.js
+++ b/eln/nucleic/genbank.js
@@ -1,7 +1,8 @@
-import Twig from 'lib/twigjs/twig';
+// eslint-disable-next-line import/no-unassigned-import
import 'angularplasmid';
-import typerenderer from 'src/util/typerenderer';
import $ from 'jquery';
+import Twig from 'lib/twigjs/twig';
+import typerenderer from 'src/util/typerenderer';
const templateOptions = {
style: `
@@ -86,9 +87,9 @@ export async function getSvg(parsedGb, options) {
}
async function compile(val) {
- return new Promise(function (resolve) {
+ return new Promise(function compile(resolve) {
let $injector = self.angular.injector(['ng', 'angularplasmid']);
- $injector.invoke(function ($rootScope, $compile) {
+ $injector.invoke(function invoke($rootScope, $compile) {
const svg = $compile(String(val))($rootScope);
// TODO: why is this setTimeout needed
setTimeout(() => resolve(svg), 0);
diff --git a/eln/pubchem/ghs.js b/eln/pubchem/ghs.js
index 92196858..75a44487 100644
--- a/eln/pubchem/ghs.js
+++ b/eln/pubchem/ghs.js
@@ -2,7 +2,7 @@ import OCL from 'openchemlib';
// returns GHS information based on pubchem and a smiles
-define(['src/util/ui', 'src/util/api'], function (UI, API) {
+define(['src/util/ui', 'src/util/api'], (UI, API) => {
async function fromIDCode(oclCode, options) {
const molecule = OCL.Molecule.fromIDCode(oclCode);
const smiles = molecule.toSmiles();
diff --git a/eln/pubchem/info.js b/eln/pubchem/info.js
index c317d077..46d5ffef 100644
--- a/eln/pubchem/info.js
+++ b/eln/pubchem/info.js
@@ -2,14 +2,14 @@ import OCL from 'openchemlib';
// returns GHS information based on pubchem and a smiles
-define(['src/util/ui', 'src/util/api'], function (UI, API) {
+define(['src/util/ui'], (UI) => {
async function fromIDCode(oclCode, options) {
const molecule = OCL.Molecule.fromIDCode(oclCode);
const smiles = molecule.toSmiles();
return fromSMILES(smiles, options);
}
- async function fromSMILES(smiles, options = {}) {
+ async function fromSMILES(smiles) {
const html = ``;
@@ -24,185 +24,3 @@ define(['src/util/ui', 'src/util/api'], function (UI, API) {
return { fromIDCode, fromSMILES };
});
-
-const ghsTemplate = `
-
-
- {% if ghs.pictograms %}
-
Pictograms
-
- {% for pictogram in ghs.pictograms %}
-
- |
- {{pictogram.code}}
- |
-
-
- {{rendertypeBlock(pictogram.code,'ghs')}}
-
- |
-
- {{pictogram.description}}
- |
-
- {% endfor %}
-
- {% endif %}
- {% if ghs.hStatements %}
-
Hazard statements
-
- {% for h in ghs.hStatements %}
-
- |
- {{h.code}}
- |
-
- {{h.description}}
- |
-
- {% endfor %}
-
- {% endif %}
- {% if ghs.pStatements %}
-
Precautionary statements
-
- {% for p in ghs.pStatements %}
-
- |
- {{p.code}}
- |
-
- {{p.description}}
- |
-
- {% endfor %}
-
- {% endif %}
-
-
Detailed safety information
- {% if ghsFull.pictograms %}
-
Pictograms
- {% for entry in ghsFull.pictograms %}
-
-
- Name: {{entry.reference.name}}
-
-
{{entry.reference.description}}
-
- {% for pictogram in entry.data %}
-
- |
- {{pictogram.code}}
- |
-
-
- {{rendertypeBlock(pictogram.code,'ghs')}}
-
- |
-
- {{pictogram.description}}
- |
-
- {% endfor %}
-
- {% endfor %}
- {% endif %}
- {% if ghsFull.hStatements %}
-
Hazard statements
- {% for entry in ghsFull.hStatements %}
-
-
- Name: {{entry.reference.name}}
-
-
{{entry.reference.description}}
-
- {% for hStatement in entry.data %}
-
- |
- {{hStatement.code}}
- |
-
- {{hStatement.description}}
- |
-
- {% endfor %}
-
- {% endfor %}
- {% endif %}
- {% if ghsFull.pStatements %}
-
Precautionary statements
- {% for entry in ghsFull.pStatements %}
-
-
- Name: {{entry.reference.name}}
-
-
{{entry.reference.description}}
-
- {% for pStatement in entry.data %}
-
- |
- {{pStatement.code}}
- |
-
- {{pStatement.description}}
- |
-
- {% endfor %}
-
- {% endfor %}
- {% endif %}
-
-
- {% for n in ${val} %}
- | {{ n${prop} }} |
- {% endfor %}
-
-
✔ |
✘ |
- =1-\sum\limits_{i=1}^{n}min(p_i,q_i))
+ =1-\\sum\\limits_{i=1}^{n}min(p_i,q_i))
|
diff --git a/eln/stock/ACI/samples.js b/eln/stock/ACI/samples.js
index 625db91d..f978b2fc 100644
--- a/eln/stock/ACI/samples.js
+++ b/eln/stock/ACI/samples.js
@@ -1,4 +1,4 @@
-module.exports = function (roc) {
+module.exports = function aciSamples(roc) {
return {
async getNextCommercialBatch(structureId) {
structureId = String(structureId);
diff --git a/eln/stock/ACI/structures.js b/eln/stock/ACI/structures.js
index 1dbc8a7d..76df4827 100644
--- a/eln/stock/ACI/structures.js
+++ b/eln/stock/ACI/structures.js
@@ -9,7 +9,7 @@ function Structure(roc) {
};
if (type) {
- options.filter = function (entry) {
+ options.filter = (entry) => {
return entry.$id[1] === type;
};
}
@@ -55,8 +55,8 @@ function Structure(roc) {
disableNotification: true,
});
return entry;
- } catch (e) {
- if (e.message === 'Conflict') {
+ } catch (err) {
+ if (err.message === 'Conflict') {
// try to get id
const result = await roc.view('entryById', {
key: [ocl.idCode, type],
@@ -64,7 +64,9 @@ function Structure(roc) {
if (result.length) {
return result[0];
} else {
- throw new Error('Unexpected error creating structure');
+ throw new Error('Unexpected error creating structure', {
+ cause: err,
+ });
}
}
}
diff --git a/eln/stock/ACI/util.js b/eln/stock/ACI/util.js
index 3efa4406..0cfd55d9 100644
--- a/eln/stock/ACI/util.js
+++ b/eln/stock/ACI/util.js
@@ -2,7 +2,7 @@ import _ from 'lodash';
import OCL from 'openchemlib';
import UI from 'src/util/ui';
-module.exports = function (roc, prefix) {
+module.exports = function aciUtil(roc, prefix) {
function getMoleculeWithSalts(options) {
const { saltCode, idCode, nbSalts, value } = options;
const oclid = idCode || value;
@@ -212,7 +212,7 @@ module.exports = function (roc, prefix) {
};
};
-var salts = {
+const salts = {
NX: {
name: 'Free base',
mf: '',
diff --git a/eln/stock/printer/LabelRanges.js b/eln/stock/printer/LabelRanges.js
index c592ddbc..4aea20bb 100644
--- a/eln/stock/printer/LabelRanges.js
+++ b/eln/stock/printer/LabelRanges.js
@@ -56,7 +56,6 @@ function expandRanges(data) {
const extensions = ['from', 'to', 'format'];
for (let key in data) {
let field;
- let value;
for (let extension of extensions) {
if (key.endsWith(`_${extension}`)) {
field = key.replace(/_.*?$/, '');
diff --git a/eln/stock/printer/PrintServer.js b/eln/stock/printer/PrintServer.js
index 6fc80f92..a01c3a33 100644
--- a/eln/stock/printer/PrintServer.js
+++ b/eln/stock/printer/PrintServer.js
@@ -1,4 +1,4 @@
-define(['superagent', 'uri/URI'], function (superagent, URI) {
+define(['superagent', 'uri/URI'], (superagent, URI) => {
class PrintServer {
constructor(server, opts) {
opts = opts || {};
diff --git a/eln/stock/printer/PrinterInstance.js b/eln/stock/printer/PrinterInstance.js
index 411f590b..8b262dcb 100644
--- a/eln/stock/printer/PrinterInstance.js
+++ b/eln/stock/printer/PrinterInstance.js
@@ -3,7 +3,7 @@ define([
'./printServerFactory',
'./printProcessors',
'../../libs/MolecularFormula',
-], function (Util, printServerFactory, processors, MolecularFormula) {
+], (Util, printServerFactory, processors, MolecularFormula) => {
class Printer {
constructor(printer, printServer, opts) {
this.url = String(printServer.url);
@@ -50,7 +50,6 @@ define([
`${result.$content.general.mf}`,
);
result.mfCanonic = mf.toMF();
- console.log(result.mfCanonic);
}
if (result.$content.general.description) {
result.line1 = result.$content.general.description.substring(
diff --git a/eln/stock/printer/ZebraPrintServer.js b/eln/stock/printer/ZebraPrintServer.js
index 34276cd6..28ba6815 100644
--- a/eln/stock/printer/ZebraPrintServer.js
+++ b/eln/stock/printer/ZebraPrintServer.js
@@ -1,4 +1,4 @@
-define(['superagent', 'uri/URI'], function (superagent, URI) {
+define(['superagent', 'uri/URI'], (superagent, URI) => {
class ZebraPrintServer {
constructor(server, opts) {
this.server = server;
diff --git a/eln/stock/printer/factory.js b/eln/stock/printer/factory.js
index 69909894..b2c9a58f 100644
--- a/eln/stock/printer/factory.js
+++ b/eln/stock/printer/factory.js
@@ -1,12 +1,12 @@
import printer from './printer';
-module.exports = function (opts, cb) {
+module.exports = function printerFactor(opts, cb) {
if (typeof opts === 'function') {
cb = opts;
opts = {};
}
if (typeof IframeBridge !== 'undefined') {
- self.IframeBridge.onMessage(async function (data) {
+ self.IframeBridge.onMessage(async (data) => {
if (data.type === 'tab.data') {
let optsCopy = { ...opts };
if (data.message.printer && data.message.printer.couchDB) {
diff --git a/eln/stock/printer/helper.js b/eln/stock/printer/helper.js
index 040f59a0..d4b1f2f4 100644
--- a/eln/stock/printer/helper.js
+++ b/eln/stock/printer/helper.js
@@ -10,7 +10,6 @@ module.exports = {
...JSON.parse(JSON.stringify(printer)),
formats: [],
}));
- console.log(varPrinterFormats);
for (let i = 0; i < printers.length; i++) {
for (let j = 0; j < types.length; j++) {
const sFormats = (await printer.getFormats(printers[i], types[j])).map(
@@ -33,7 +32,6 @@ module.exports = {
await API.createData(`${types[j]}Formats`, varFormats[j]);
}
API.createData('varPrinterFormats', varPrinterFormats);
- console.log(varPrinterFormats);
},
async askPrintEntry(entry, type) {
diff --git a/eln/stock/printer/printProcessors.js b/eln/stock/printer/printProcessors.js
index 99f4400d..2c432e23 100644
--- a/eln/stock/printer/printProcessors.js
+++ b/eln/stock/printer/printProcessors.js
@@ -5,7 +5,7 @@ define([
'canvg',
'../../libs/Image',
'openchemlib',
-], function (Datas, UI, twig, canvg, IJS, OCL) {
+], (Datas, UI, twig, canvg, IJS, OCL) => {
IJS = IJS.default;
const DataObject = Datas.DataObject;
let chars =
@@ -175,12 +175,12 @@ define([
return decode(bmp);
}
- function concatenate(resultConstructor, ...arrays) {
+ function concatenate(ResultConstructor, ...arrays) {
let totalLength = 0;
for (let arr of arrays) {
totalLength += arr.length;
}
- let result = new resultConstructor(totalLength);
+ let result = new ResultConstructor(totalLength);
let offset = 0;
for (let arr of arrays) {
result.set(arr, offset);
@@ -221,7 +221,7 @@ define([
function dataToHexa(arr) {
return Array.prototype.map
- .call(arr, function (n) {
+ .call(arr, (n) => {
let hex = n.toString(16);
if (hex.length === 1) hex = `0${hex}`;
return hex;
diff --git a/eln/stock/printer/printer.js b/eln/stock/printer/printer.js
index a659ce1f..b4735642 100644
--- a/eln/stock/printer/printer.js
+++ b/eln/stock/printer/printer.js
@@ -4,11 +4,11 @@ define([
'./printProcessors',
'./printServerFactory',
'../../../rest-on-couch/Roc',
-], function (API, Printer, processors, printServerFactory, Roc) {
+], (API, Printer, processors, printServerFactory, Roc) => {
const SECOND = 1000;
const MINUTE = 60 * SECOND;
const LIMIT = 11 * MINUTE;
- return async function (opts) {
+ return async function stockPrinter(opts) {
let printerRoc,
formatsRoc,
printServerRoc,
@@ -88,7 +88,7 @@ define([
// printerFormat: uuid of the printer format or printer format document
async print(printer, printFormat, data) {
- printer = await printerRoc.get(printer);
+ const dbPrinter = await printerRoc.get(printer);
if (printFormat.resurrect) {
printFormat = printFormat.resurrect();
}
@@ -99,9 +99,9 @@ define([
const printServer = printServers.find(
(ps) =>
String(ps.$content.macAddress) ===
- String(printer.$content.macAddress),
+ String(dbPrinter.$content.macAddress),
);
- const p = new Printer(printer.$content, printServer.$content, opts);
+ const p = new Printer(dbPrinter.$content, printServer.$content, opts);
await p.print(printFormat.$content, data);
},
@@ -139,7 +139,7 @@ define([
// get online printers that can print a given format
async getPrinters(format) {
if (!format) return onlinePrinters;
- format = await formatsRoc.get(format);
+ const dbFormat = await formatsRoc.get(format);
const onlineMacAdresses = onlinePrinters.map(
(ps) => ps.$content.macAddress,
);
@@ -147,7 +147,7 @@ define([
.filter((p) => onlineMacAdresses.includes(p.$content.macAddress))
.filter((p) => {
return (
- format.$content.models.filter(
+ dbFormat.$content.models.filter(
(m) => String(m.name) === String(p.$content.model),
).length > 0
);
@@ -155,8 +155,9 @@ define([
},
async getFormats(printer, type) {
+ let formats;
if (!printer) {
- var formats = printFormats.filter((f) => {
+ formats = printFormats.filter((f) => {
return onlinePrinters.some((printer) =>
f.$content.models.some(
(m) => String(m.name) === String(printer.$content.model),
@@ -164,10 +165,10 @@ define([
);
});
} else {
- printer = await printerRoc.get(printer);
+ const dbPrinter = await printerRoc.get(printer);
formats = printFormats.filter((f) =>
f.$content.models.some(
- (m) => String(m.name) === String(printer.$content.model),
+ (m) => String(m.name) === String(dbPrinter.$content.model),
),
);
}
diff --git a/eln/stock/search/chemexper.js b/eln/stock/search/chemexper.js
index faf8e89d..3433bc68 100644
--- a/eln/stock/search/chemexper.js
+++ b/eln/stock/search/chemexper.js
@@ -1,4 +1,3 @@
-import _ from 'lodash';
import ui from 'src/util/ui';
import util from 'src/util/util';
import superagent from 'superagent';
diff --git a/eln/stock/search/chemspider.js b/eln/stock/search/chemspider.js
index aa238599..49d68815 100644
--- a/eln/stock/search/chemspider.js
+++ b/eln/stock/search/chemspider.js
@@ -32,10 +32,10 @@ function fromChemspider(chemspider) {
source: 'chemspider',
};
- const name = (entry.$content.general.name = []);
- const identifier = (entry.$content.identifier = {});
- const cas = (identifier.cas = []);
- const CSID = (identifier.chemSpiderID = []);
+ const name = entry.$content.general.name ?? [];
+ const identifier = entry.$content.identifier ?? {};
+ const cas = identifier.cas ?? [];
+ const CSID = identifier.chemSpiderID ?? [];
const synonyms = chemspider.Synonyms;
for (let i = 0; i < synonyms.length; i++) {
const synonym = synonyms[i];
diff --git a/eln/stock/search/epfl.js b/eln/stock/search/epfl.js
index 092276e2..c8a071ef 100644
--- a/eln/stock/search/epfl.js
+++ b/eln/stock/search/epfl.js
@@ -13,7 +13,7 @@ module.exports = {
term,
)}`,
)
- .then(function (result) {
+ .then((result) => {
result = result.body && result.body.entry;
if (!result) {
ui.showNotification('No results in reference DB', 'warn');
diff --git a/eln/stock/search/search.js b/eln/stock/search/search.js
index 639167fa..8228ca74 100644
--- a/eln/stock/search/search.js
+++ b/eln/stock/search/search.js
@@ -33,7 +33,6 @@ module.exports = {
endkey: ['sample', [`${term}\ufff0`, {}]],
})
.then((data) => {
- console.log(data);
data.forEach((d) => {
const status =
d.$content &&
@@ -129,8 +128,8 @@ module.exports = {
rowHeight: 150,
},
})
- .catch(function (e) {
- console.error(e); // eslint-disable-line no-console
+ .catch((err) => {
+ reportError(err);
ui.showNotification('search failed', 'error');
});
},
diff --git a/eln/structureSearch/fromFile.js b/eln/structureSearch/fromFile.js
index e5f8811a..a16759b1 100644
--- a/eln/structureSearch/fromFile.js
+++ b/eln/structureSearch/fromFile.js
@@ -4,7 +4,7 @@ import { OCL, OCLUtils } from '../libs/OCLUtils';
function waitImmediate() {
return new Promise((resolve) => {
- setImmediate(resolve);
+ window.setImmediate(resolve);
});
}
diff --git a/eln/taxonomy/renderer.js b/eln/taxonomy/renderer.js
index 8e88f244..7a159d85 100644
--- a/eln/taxonomy/renderer.js
+++ b/eln/taxonomy/renderer.js
@@ -4,7 +4,6 @@ import { createTaxonomyTree } from '../../../../../../../../lib/mass-tools/7.8.2
import * as TreeSVG from '../../../../../../../../lib/react-tree-svg/0.1.1/react-tree-svg';
export function add() {
- console.log(TreeSVG);
TypeRenderer.addType('taxonomyTree', {
toscreen($element, val, root, options = {}) {
let taxonomies = val.code || val;
diff --git a/eln/templates/TemplatesManager.js b/eln/templates/TemplatesManager.js
index 5f1769a0..4a6d16dc 100644
--- a/eln/templates/TemplatesManager.js
+++ b/eln/templates/TemplatesManager.js
@@ -4,7 +4,7 @@ define([
'src/util/api',
'vh/rest-on-couch/showRecordInfo',
'src/util/ui',
-], function (Roc, getChangedGroups, API, showRecordInfo, UI) {
+], (Roc, getChangedGroups, API, showRecordInfo, UI) => {
class TemplatesManager {
/**
*
@@ -29,7 +29,6 @@ define([
}
async updateTemplate() {
- console.log('UPDATE TEMPLATE');
const template = API.getData('currentTemplate');
await this.roc.update(template.value);
this.refreshTemplates();
@@ -47,7 +46,7 @@ define([
this.refreshTemplates();
}
- async createTemplate(options = {}) {
+ async createTemplate() {
const form = await UI.form(
`
@@ -102,7 +101,6 @@ define([
const template = await this.roc.create(templateEntry);
await this.refreshTemplates();
- console.log(template);
return template;
}
@@ -140,8 +138,6 @@ define([
let actionName = action.name;
let actionValue = action.value;
- console.log('ACTION:', actionName, actionValue);
-
switch (actionName) {
case 'createTemplate':
return this.createTemplate(options);
@@ -157,6 +153,10 @@ define([
return this.editTemplateAccess(actionValue);
case 'refreshTemplates':
return this.refreshTemplates();
+ default: {
+ // eslint-disable-next-line no-console
+ console.log(`TemplatesManager: unhandled action ${actionName}`);
+ }
}
}
@@ -178,8 +178,6 @@ define([
async showTemplateInfo(entry) {
const record = await this.roc.get(entry.id);
- console.log('got record');
- console.log({ record });
return showRecordInfo(record);
}
}
diff --git a/eln/templates/load.js b/eln/templates/load.js
index b677078e..66dc2213 100644
--- a/eln/templates/load.js
+++ b/eln/templates/load.js
@@ -18,20 +18,22 @@ module.exports = async function load(categories, options = {}) {
let templates;
if (roc) {
- await fetch(`${roc.url}/db/templates/_query/template?key=abcdef`)
- .then(async (result) => {
- if (result.status === 200) {
- templates = await fetchAndLink(`${roc.url}`, categories);
- if (!templates || templates.length === 0) {
- templates = await fetchPublicAndLink(categories);
- }
- } else {
+ const result = await fetch(
+ `${roc.url}/db/templates/_query/template?key=abcdef`,
+ );
+
+ if (result.status === 200) {
+ try {
+ templates = await fetchAndLink(`${roc.url}`, categories);
+ if (!templates || templates.length === 0) {
templates = await fetchPublicAndLink(categories);
}
- })
- .catch(async () => {
+ } catch {
templates = await fetchPublicAndLink(categories);
- });
+ }
+ } else {
+ templates = await fetchPublicAndLink(categories);
+ }
} else {
templates = await fetchPublicAndLink(categories);
}
@@ -78,7 +80,10 @@ async function fetchPublicAndLink(categories) {
return templates;
}
-async function fetchAndLink(url = 'https://mydb.cheminfo.org', categories) {
+async function fetchAndLink(
+ url = 'https://mydb.cheminfo.org',
+ categories = undefined,
+) {
let templates = [];
for (let category of categories) {
let startkey = category;
diff --git a/eln/templates/loadTwig.js b/eln/templates/loadTwig.js
index 0f4e7819..0913c22c 100644
--- a/eln/templates/loadTwig.js
+++ b/eln/templates/loadTwig.js
@@ -6,7 +6,7 @@ module.exports = async function loadTwig(category, options = {}) {
const { variableName = 'twigTemplate' } = options;
try {
- let templates = DataObject(await load(category));
+ let templates = new DataObject(await load(category));
let twigTemplate = await templates.getChild([
'0',
'document',
@@ -15,9 +15,8 @@ module.exports = async function loadTwig(category, options = {}) {
]);
if (variableName) API.createData(variableName, twigTemplate);
return twigTemplate;
- } catch (e) {
- // eslint-disable-next-line no-console
- console.log(`No twig format found for ${category}`);
+ } catch (err) {
+ reportError(err);
return '';
}
};
diff --git a/eln/util/appendedDragAndDrop.js b/eln/util/appendedDragAndDrop.js
index 30c96830..c813d748 100644
--- a/eln/util/appendedDragAndDrop.js
+++ b/eln/util/appendedDragAndDrop.js
@@ -32,7 +32,7 @@ export function appendedDragAndDrop(experimentalFiles, targetName) {
target.push({ file });
}
} else {
- var type;
+ let type;
if (String(file.encoding) === 'text') {
type = getTargetType(String(file.content));
} else {
diff --git a/eln/util/jcampInfo.js b/eln/util/jcampInfo.js
index 0cbbb4b2..df0ae223 100644
--- a/eln/util/jcampInfo.js
+++ b/eln/util/jcampInfo.js
@@ -9,8 +9,6 @@ async function jcampInfo(value) {
keepRecordsRegExp: /.*/,
}).flatten[0];
- console.log(parsed);
-
let data = [];
for (let key of Object.keys(parsed.meta)) {
diff --git a/eln/util/newSampleDialog.js b/eln/util/newSampleDialog.js
index 473d0c9a..fee5ecef 100644
--- a/eln/util/newSampleDialog.js
+++ b/eln/util/newSampleDialog.js
@@ -1,4 +1,4 @@
-define(['src/util/ui', 'lodash'], function (ui, _) {
+define(['src/util/ui', 'lodash'], (ui, _) => {
return async function createSample(roc, allGroups) {
const storageKey = 'eln-new-sample-default-groups';
let entrysample = { $content: {} };
diff --git a/eln/zenodo/ZenodoUtils.js b/eln/zenodo/ZenodoUtils.js
index 65d760ea..4d87cff0 100644
--- a/eln/zenodo/ZenodoUtils.js
+++ b/eln/zenodo/ZenodoUtils.js
@@ -229,7 +229,7 @@ export function getReadmeForDeposition(ZenodoDeposition) {
'',
);
if (Array.isArray(meta.creators) && meta.creators.length > 0) {
- for (const [i, c] of meta.creators.entries()) {
+ for (const [, c] of meta.creators.entries()) {
const identifiers = c.person_or_org.identifiers || [];
if (identifiers.length === 0) {
identifiers.push({ scheme: 'orcid', identifier: '' });
@@ -255,7 +255,7 @@ export function getReadmeForDeposition(ZenodoDeposition) {
}
if (Array.isArray(meta.contributors) && meta.contributors.length > 0) {
md.push('', `## Contributors`, '');
- for (const [i, c] of meta.contributors.entries()) {
+ for (const [, c] of meta.contributors.entries()) {
md.push(
`- [**${c.person_or_org.name}**${
c.affiliations[0].name
@@ -440,6 +440,7 @@ function getAdditionalDescription(description) {
break;
}
}
+ return outputHTML;
}
export function getKeywordsForDeposition(samples) {
diff --git a/eslint.config.mjs b/eslint.config.mjs
index 2e98d653..53f345ea 100644
--- a/eslint.config.mjs
+++ b/eslint.config.mjs
@@ -6,8 +6,9 @@ export default defineConfig(
globalIgnores([
'node_modules',
'build',
- 'tiles/font-awesome',
+
// Ignore third-party libraries
+ 'tiles/font-awesome',
'util/aesjs.js',
'util/cloneDeepLimitArray.js',
'util/md5.js',
@@ -33,6 +34,8 @@ export default defineConfig(
'import/no-extraneous-dependencies': 'off',
'import/no-named-as-default': 'off',
'import/no-named-as-default-member': 'off',
+ 'no-await-in-loop': 'warn',
+ 'prefer-named-capture-group': 'off',
},
},
);
diff --git a/moocs/answer.js b/moocs/answer.js
index b2c3d5bd..e20a9293 100644
--- a/moocs/answer.js
+++ b/moocs/answer.js
@@ -1,7 +1,8 @@
-define(['mathjs'], function (mathjs) {
+define(['mathjs'], (mathjs) => {
let exports = {};
- exports.isCorrect = function (sol, ans, options) {
+ exports.isCorrect = function isCorrect(sol, ans, options) {
+ let errorUnit, solUnit, ansUnit, solU;
sol = String(sol);
ans = String(ans);
options = { ...options };
@@ -11,7 +12,7 @@ define(['mathjs'], function (mathjs) {
if (options.absoluteError !== undefined) {
options.absoluteError = String(options.absoluteError);
try {
- var errorUnit = mathjs.unit(options.absoluteError);
+ errorUnit = mathjs.unit(options.absoluteError);
} catch (e) {
if (e.message.match(/no units/)) {
options.absoluteError = +options.absoluteError;
@@ -22,7 +23,7 @@ define(['mathjs'], function (mathjs) {
}
try {
- var solUnit = mathjs.unit(String(sol));
+ solUnit = mathjs.unit(String(sol));
} catch (e) {
if (e.message.match(/no units/)) {
sol = +sol;
@@ -33,7 +34,7 @@ define(['mathjs'], function (mathjs) {
reason: 'did not expect units in answer',
};
} else {
- return isCorrect(sol, ans, options);
+ return checkCorrectness(sol, ans, options);
}
} else {
return {
@@ -44,8 +45,8 @@ define(['mathjs'], function (mathjs) {
}
try {
- var ansUnit = mathjs.unit(String(ans));
- var solU = solUnit.formatUnits();
+ ansUnit = mathjs.unit(String(ans));
+ solU = solUnit.formatUnits();
} catch (e) {
return {
correct: false,
@@ -64,14 +65,14 @@ define(['mathjs'], function (mathjs) {
if (errorUnit) {
options.absoluteError = errorUnit.toNumber(solU);
}
- return isCorrect(sol, ans, options);
+ return checkCorrectness(sol, ans, options);
}
};
return exports;
});
-function isCorrect(sol, ans, options) {
+function checkCorrectness(sol, ans, options) {
let absoluteError =
options.absoluteError !== undefined && !isNaN(options.absoluteError)
? options.absoluteError
diff --git a/moocs/exercisesManager.js b/moocs/exercisesManager.js
index e3e53657..aec5f4d4 100644
--- a/moocs/exercisesManager.js
+++ b/moocs/exercisesManager.js
@@ -1,4 +1,4 @@
-define(['src/util/api'], function (API) {
+define(['src/util/api'], (API) => {
async function exercisesManager(action, allExercises, options) {
switch (action) {
case 'init': {
@@ -60,8 +60,8 @@ define(['src/util/api'], function (API) {
saveState(options.cookieName, state);
return API.createData('exercises', selectedExercises).then(
- function (exercises) {
- exercises.onChange(function (evt) {
+ (exercises) => {
+ exercises.onChange((evt) => {
if (evt.target.__name === 'myResult') {
let target = evt.target.__parent;
if (target) {
diff --git a/moocs/stoechiometry.js b/moocs/stoechiometry.js
index 78e0cbf3..bb050546 100644
--- a/moocs/stoechiometry.js
+++ b/moocs/stoechiometry.js
@@ -1,41 +1,41 @@
define([
'https://www.lactame.com/lib/chemcalc/3.0.6/chemcalc.js',
'https://www.lactame.com/lib/ml/1.0.0/ml.js',
-], function (CC, ml) {
+], (CC, ml) => {
let exports = {};
- exports.findCoefficients = function (reagents, products) {
+ exports.findCoefficients = function findCoefficient(reagents, products) {
let atoms = {};
let nbCoeff = reagents.length + products.length;
let matrix = new Array(nbCoeff);
- for (var i = 0; i < nbCoeff; i++) {
+ for (let i = 0; i < nbCoeff; i++) {
matrix[i] = [];
}
- for (i = 0; i < reagents.length; i++) {
- var c = CC.analyseMF(reagents[i]);
- var part = c.parts[0];
- for (var k = 0; k < part.ea.length; k++) {
- var ea = part.ea[k];
+ for (let i = 0; i < reagents.length; i++) {
+ const c = CC.analyseMF(reagents[i]);
+ const part = c.parts[0];
+ for (let k = 0; k < part.ea.length; k++) {
+ const ea = part.ea[k];
atoms[ea.element] = true;
- var idx = Object.keys(atoms).indexOf(ea.element);
+ const idx = Object.keys(atoms).indexOf(ea.element);
matrix[i][idx] = part.ea[k].number;
}
}
- for (i = reagents.length; i < nbCoeff; i++) {
- c = CC.analyseMF(products[i - reagents.length]);
- part = c.parts[0];
- for (k = 0; k < part.ea.length; k++) {
- ea = part.ea[k];
+ for (let i = reagents.length; i < nbCoeff; i++) {
+ const c = CC.analyseMF(products[i - reagents.length]);
+ const part = c.parts[0];
+ for (let k = 0; k < part.ea.length; k++) {
+ const ea = part.ea[k];
atoms[ea.element] = true;
- idx = Object.keys(atoms).indexOf(ea.element);
+ const idx = Object.keys(atoms).indexOf(ea.element);
matrix[i][idx] = part.ea[k].number;
}
}
let nbAtoms = Object.keys(atoms).length;
- for (i = 0; i < nbCoeff; i++) {
+ for (let i = 0; i < nbCoeff; i++) {
for (let j = 0; j < nbAtoms; j++) {
if (matrix[i][j] === undefined) {
matrix[i][j] = 0;
@@ -51,9 +51,9 @@ define([
let result;
if (!matrix.isSquare()) {
if (matrix.rows - matrix.columns === -1) {
- var trivialRow = new Array(matrix.columns).fill(0);
+ const trivialRow = new Array(matrix.columns).fill(0);
trivialRow[0] = 1;
- var e = new Array(matrix.columns).fill([0]);
+ const e = new Array(matrix.columns).fill([0]);
e[matrix.columns - 1] = [1];
matrix.addRow(matrix.rows, trivialRow);
@@ -62,13 +62,14 @@ define([
console.warn('cannot solve'); // eslint-disable-line no-console
}
} else {
- let LU = ml.Matrix.Decompositions.LU(matrix);
+ // eslint-disable-next-line new-cap
+ const LU = ml.Matrix.Decompositions.LU(matrix);
if (LU.isSingular()) {
let diag0Pos = findDiag0Pos(LU.LU);
- idx = LU.pivotVector.indexOf(diag0Pos);
- trivialRow = new Array(matrix.columns).fill(0);
+ const idx = LU.pivotVector.indexOf(diag0Pos);
+ const trivialRow = new Array(matrix.columns).fill(0);
trivialRow[idx] = 1;
- e = new Array(matrix.columns).fill([0]);
+ const e = new Array(matrix.columns).fill([0]);
e[idx] = [1];
matrix.setRow(idx, trivialRow);
result = matrix.solve(e);
@@ -81,15 +82,15 @@ define([
return result;
};
- exports.formatResult = function (reagents, products, result) {
+ exports.formatResult = function formatResult(reagents, products, result) {
let rstr = reagents
- .map(function (value, index) {
+ .map((value, index) => {
return `${result[index]}${value}`;
})
.join(' + ');
let pstr = products
- .map(function (value, index) {
+ .map((value, index) => {
return `${
result[reagents.length + index]
}${value}`;
diff --git a/on-tabs/.eslintrc.yml b/on-tabs/.eslintrc.yml
deleted file mode 100644
index add5a785..00000000
--- a/on-tabs/.eslintrc.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-parserOptions:
- sourceType: module
diff --git a/on-tabs/util.js b/on-tabs/util.js
index 05b1c33d..8fd50d52 100644
--- a/on-tabs/util.js
+++ b/on-tabs/util.js
@@ -26,8 +26,8 @@ function onRocInit(data) {
return false;
}
-function onDataFocus(dataId, tabId, type) {
- return function (data) {
+function createOnDataFocus(dataId, tabId, type) {
+ return function onDataFocus(data) {
if (data.type === 'tab.focus') {
let data;
if (type === 'data') data = API.getData(dataId);
@@ -51,10 +51,10 @@ module.exports = {
});
},
sendCacheOnFocus(dataId, tabId) {
- IB.onMessage(onDataFocus(dataId, tabId, 'cache'));
+ IB.onMessage(createOnDataFocus(dataId, tabId, 'cache'));
},
sendDataOnFocus(dataId, tabId) {
- IB.onMessage(onDataFocus(dataId, tabId, 'data'));
+ IB.onMessage(createOnDataFocus(dataId, tabId, 'data'));
},
sendVariableOnChange(data, tabId) {
data.onChange((event) => {
@@ -75,7 +75,7 @@ module.exports = {
},
// register callback to handle message of type 'message', without info about the sender
onMessage(cb) {
- IB.onMessage(function (data) {
+ IB.onMessage((data) => {
if (data.type === 'tab.message') {
cb(data.message);
}
diff --git a/package.json b/package.json
index 0dddb4d3..8d3e0b19 100644
--- a/package.json
+++ b/package.json
@@ -4,7 +4,7 @@
"version": "0.0.0",
"description": "",
"scripts": {
- "babel": "babel . --out-dir ./build",
+ "babel-test": "babel . --config-file=./test-build.babel.mjs --out-dir ./build",
"eslint": "eslint . --cache",
"eslint-fix": "npm run eslint -- --fix",
"prettier": "prettier --check .",
diff --git a/rest-on-couch/Roc.js b/rest-on-couch/Roc.js
index 68c2edb8..68329be4 100644
--- a/rest-on-couch/Roc.js
+++ b/rest-on-couch/Roc.js
@@ -13,7 +13,7 @@ define([
'eventEmitter',
'./UserViewPrefs',
'./UserAnalysisResults',
-], function (
+], (
Datas,
API,
ui,
@@ -28,14 +28,14 @@ define([
EventEmitter,
UserViewPrefs,
UserAnalysisResults,
-) {
+) => {
const DataObject = Datas.DataObject;
const eventEmitters = {};
const objectHasOwnProperty = Object.prototype.hasOwnProperty;
- const hasOwnProperty = function (obj, prop) {
+ function hasOwnProperty(obj, prop) {
return objectHasOwnProperty.call(obj, prop);
- };
+ }
function setTabSavedStatus(saved) {
if (self.IframeBridge) {
@@ -220,7 +220,7 @@ define([
credentials: 'include',
})
).json();
- } catch (e) {
+ } catch {
this.setUserPrefs(defaultPrefs);
return defaultPrefs;
}
@@ -288,8 +288,8 @@ define([
}
return res.body;
})
- .then(handleSuccess(this, options))
- .catch(handleError(this, options));
+ .then(createHandleSuccess(this, options))
+ .catch(createHandleError(this, options));
}
async queryBySampleId(options) {
@@ -314,8 +314,8 @@ define([
}
return res.body;
})
- .then(handleSuccess(this, options))
- .catch(handleError(this, options));
+ .then(createHandleSuccess(this, options))
+ .catch(createHandleError(this, options));
}
async query(viewName, options) {
@@ -372,8 +372,8 @@ define([
}
return res.body;
})
- .then(handleSuccess(this, options))
- .catch(handleError(this, options));
+ .then(createHandleSuccess(this, options))
+ .catch(createHandleError(this, options));
}
getDocumentEventEmitter(uuid) {
@@ -499,8 +499,8 @@ define([
return res.body;
}
return null;
- } catch (e) {
- handleError(this, options);
+ } catch {
+ createHandleError(this, options);
return null;
}
}
@@ -519,7 +519,7 @@ define([
}
return null;
})
- .catch(handleError(this, options))
+ .catch(createHandleError(this, options))
);
}
@@ -546,7 +546,7 @@ define([
}
return null;
})
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async getById(id, options) {
@@ -556,7 +556,7 @@ define([
if (!entry || options.fromCache) {
return entry;
}
- return this.get(entry).catch(handleError(this, options));
+ return this.get(entry).catch(createHandleError(this, options));
}
// Get the groups the user is owner of
@@ -571,7 +571,7 @@ define([
.get(groupUrl)
.withCredentials()
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
// Get basic info about every group (only name and description)
@@ -586,7 +586,7 @@ define([
.get(groupsInfoUrl)
.withCredentials()
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
// Get the groups the user is member of
@@ -599,7 +599,7 @@ define([
.get(url)
.withCredentials()
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async create(entry, options) {
@@ -613,7 +613,7 @@ define([
.post(this.entryUrl)
.withCredentials()
.send(entry)
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => {
if (res.body && (res.status === 200 || res.status === 201)) {
return this.get(res.body.id);
@@ -639,7 +639,7 @@ define([
}
return entry;
})
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async getLastRevision(entry) {
@@ -657,7 +657,7 @@ define([
.put(`${this.entryUrl}/${String(entry._id)}`)
.withCredentials()
.send(reqEntry)
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => {
if (res.body && res.status === 200) {
entry._rev = res.body.rev;
@@ -672,14 +672,14 @@ define([
}
return entry;
})
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async deleteAttachment(entry, attachments, options) {
await this.__ready;
options = createOptions(options, 'deleteAttachment');
if (DataObject.getType(entry) !== 'object') {
- handleError(this, options)(new Error('invalid argument'));
+ createHandleError(this, options)(new Error('invalid argument'));
return null;
}
if (Array.isArray(attachments) && attachments.length === 0) return entry;
@@ -706,10 +706,10 @@ define([
await this.update(entry, options);
} else if (entry.triggerChange && !options.noTrigger) {
entry.triggerChange();
- handleSuccess(this, options)(entry);
+ createHandleSuccess(this, options)(entry);
}
} catch (e) {
- return handleError(this, options)(e);
+ return createHandleError(this, options)(e);
}
return entry;
}
@@ -803,9 +803,9 @@ define([
this.typeUrl(entry.$content, entry);
await this.update(entry);
} catch (e) {
- return handleError(this, attachOptions)(e);
+ return createHandleError(this, attachOptions)(e);
}
- handleSuccess(this, attachOptions)(entry);
+ createHandleSuccess(this, attachOptions)(entry);
return entry;
}
@@ -837,9 +837,9 @@ define([
this.typeUrl(entry.$content, entry);
await this.update(entry);
} catch (e) {
- return handleError(this, attachOptions)(e);
+ return createHandleError(this, attachOptions)(e);
}
- handleSuccess(this, attachOptions)(entry);
+ createHandleSuccess(this, attachOptions)(entry);
return entry;
}
@@ -855,7 +855,7 @@ define([
});
try {
await idb.delete(uuid);
- } catch (e) {
+ } catch {
// ignored error
}
// Track data again
@@ -868,7 +868,7 @@ define([
await this.__ready;
options = createOptions(options, 'getAttachment');
const cdb = this._getCdb(entry);
- return cdb.get(name, options).catch(handleError(this, options));
+ return cdb.get(name, options).catch(createHandleError(this, options));
}
async getAttachmentList(entry) {
@@ -933,9 +933,9 @@ define([
entry.triggerChange();
}
} catch (e) {
- return handleError(this, options)(e);
+ return createHandleError(this, options)(e);
}
- handleSuccess(this, options)(entry);
+ createHandleSuccess(this, options)(entry);
return entry;
}
@@ -957,9 +957,9 @@ define([
return superagent
.get(tokenUrl)
.withCredentials()
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async getToken(token, options) {
@@ -973,9 +973,9 @@ define([
return superagent
.get(tokenUrl)
.withCredentials()
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async createToken(entry, options) {
@@ -993,9 +993,9 @@ define([
request.query({ rights });
}
return request
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async createUserToken(options) {
@@ -1012,9 +1012,9 @@ define([
request.query({ rights });
}
return request
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async deleteToken(token, options) {
@@ -1028,9 +1028,9 @@ define([
return superagent
.del(tokenUrl)
.withCredentials()
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => res.body)
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
async addGroup(entry, group, options, remove) {
@@ -1046,7 +1046,7 @@ define([
`${this.entryUrl}/${uuid}/_owner/${String(group)}`,
)
.withCredentials()
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => {
if (!options.noUpdate) {
return this.get(uuid).then(() => res.body);
@@ -1054,7 +1054,7 @@ define([
return res.body;
}
})
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
deleteGroup(entry, group, options) {
@@ -1068,7 +1068,7 @@ define([
return superagent
.del(`${this.entryUrl}/${uuid}`)
.withCredentials()
- .then(handleSuccess(this, options))
+ .then(createHandleSuccess(this, options))
.then((res) => {
if (res.body && res.status === 200) {
for (let key in this.variables) {
@@ -1083,7 +1083,7 @@ define([
}
return res.body;
})
- .catch(handleError(this, options));
+ .catch(createHandleError(this, options));
}
remove(entry, options) {
@@ -1256,7 +1256,7 @@ define([
if (!Array.isArray(filename) && typeof filename !== 'undefined') {
filename = [filename];
}
- this._traverseFilename(v, function (v) {
+ this._traverseFilename(v, (v) => {
if (typeof filename === 'undefined') {
r.push(v);
} else if (filename.indexOf(String(v.filename)) !== -1) {
@@ -1333,8 +1333,8 @@ define([
return options;
}
- function handleError(ctx, options) {
- return function (err) {
+ function createHandleError(ctx, options) {
+ return function handleError(err) {
if (!options.mute || !options.muteError) {
if (err.status || err.timeout) {
// error comes from superagent
@@ -1348,8 +1348,8 @@ define([
};
}
- function handleSuccess(ctx, options) {
- return function (data) {
+ function createHandleSuccess(ctx, options) {
+ return function handleSuccess(data) {
if (!options.mute && !options.muteSuccess) {
if (data.status) {
handleSuperagentSuccess(data, ctx, options);
diff --git a/rest-on-couch/UserAnalysisResults.js b/rest-on-couch/UserAnalysisResults.js
index 16bac685..f271f62c 100644
--- a/rest-on-couch/UserAnalysisResults.js
+++ b/rest-on-couch/UserAnalysisResults.js
@@ -1,8 +1,7 @@
-define([
- '../util/getViewInfo',
- 'src/util/api',
- 'src/util/couchdbAttachments',
-], function (getViewInfo, API) {
+define(['../util/getViewInfo', 'src/util/api', 'src/util/couchdbAttachments'], (
+ getViewInfo,
+ API,
+) => {
class UserAnalysisResults {
constructor(roc, sampleID) {
this.roc = roc;
@@ -38,7 +37,10 @@ define([
*/
async loadResults(key, options = {}) {
if (!this.roc) {
- console.log('Can not retrieve results, not connected to roc');
+ // eslint-disable-next-line no-console
+ console.log(
+ 'UserAnalysisResults: cannnot retrieve results, not connected to roc',
+ );
return;
}
const { sampleID = this.sampleID } = options;
@@ -59,7 +61,6 @@ define([
/* if (sampleID) {
return entries.filter((entry) => entry.$id[2].match(/^[0-9a-f]{32}$/i));
}*/
- console.log({ entries });
return entries;
}
@@ -78,7 +79,6 @@ define([
return loadTemplateFromLocalStorage(this.viewID, String(entry._id));
}
this.lastEntry = entry;
- console.log(this.lastEntry);
return this.roc.getAttachment(entry, 'result.json');
}
@@ -106,7 +106,6 @@ define([
if (!entry._id) entry._id = entry.id;
entry = await this.roc.get(entry);
entry.$content = meta;
- console.log({ entry });
await this.roc.update(entry);
} else {
entry = await this.roc.create({
diff --git a/rest-on-couch/UserViewPrefs.js b/rest-on-couch/UserViewPrefs.js
index c2595bc0..2d0839c7 100644
--- a/rest-on-couch/UserViewPrefs.js
+++ b/rest-on-couch/UserViewPrefs.js
@@ -1,4 +1,4 @@
-define(['../util/getViewInfo'], function (getViewInfo) {
+define(['../util/getViewInfo'], (getViewInfo) => {
class UserViewPrefs {
constructor(roc) {
this.roc = roc;
diff --git a/rest-on-couch/factory.js b/rest-on-couch/factory.js
index 97b42402..fa9d0b67 100644
--- a/rest-on-couch/factory.js
+++ b/rest-on-couch/factory.js
@@ -1,11 +1,11 @@
-define(['./Roc'], function (Roc) {
- return function (opts, cb) {
+define(['./Roc'], (Roc) => {
+ return function rocFactory(opts, cb) {
if (typeof opts === 'function') {
cb = opts;
opts = {};
}
if (typeof IframeBridge !== 'undefined') {
- self.IframeBridge.onMessage(function (data) {
+ self.IframeBridge.onMessage((data) => {
if (data.type === 'tab.data') {
if (data.message.couchDB) {
const options = { ...data.message.couchDB, ...opts };
diff --git a/rest-on-couch/getChangedGroups.js b/rest-on-couch/getChangedGroups.js
index 1949d332..0ef33e0e 100644
--- a/rest-on-couch/getChangedGroups.js
+++ b/rest-on-couch/getChangedGroups.js
@@ -1,4 +1,4 @@
-define(['src/util/ui', 'lodash'], function (UI, _) {
+define(['src/util/ui', 'lodash'], (UI, _) => {
function editGroups(record, allGroups) {
const groups = JSON.parse(JSON.stringify(allGroups));
const groupNames = groups.map((group) => group.name);
@@ -43,7 +43,7 @@ define(['src/util/ui', 'lodash'], function (UI, _) {
`,
{ groups },
{ twig: { groups } },
- ).then(function (result) {
+ ).then((result) => {
if (!result) return undefined;
let groups = result.groups;
let add = groups
diff --git a/rest-on-couch/showRecordInfo.js b/rest-on-couch/showRecordInfo.js
index d6e44d98..1e1ab89c 100644
--- a/rest-on-couch/showRecordInfo.js
+++ b/rest-on-couch/showRecordInfo.js
@@ -1,4 +1,4 @@
-define(['src/util/ui'], function (UI) {
+define(['src/util/ui'], (UI) => {
function showRecordInfo(record) {
let html = '';
html += `