Added more strict js linting

.eslintrc.js

@@ -8,12 +8,83 @@ module.exports = {
   },
   extends: 'eslint:recommended',
   parserOptions: {
-    ecmaVersion: 8
+    ecmaVersion: 8,
+    ecmaFeatures: {
+      impliedScrict: true
+    }
   },
   rules: {
-    semi: ['error', 'always'], // Always have semi-colons.
-    'no-console': 'error', // Don't allow console.log().
-    'no-var': 'error', // Use let or const.
+    // Potential errors.
+    'semi': 'error',
+    'curly': 'error',
+    'no-else-return': 'error',
+    'no-eq-null': 'error',
+    'no-eval': 'error',
+    'no-implied-eval': 'error',
+    'no-labels': 'error',
+    'no-console': 'error',
+    'no-var': 'error',
+    'no-warning-comments': 'warn',
+    'max-depth': [
+      'error', 
+      5
+    ],
+    'no-mixed-operators': [
+      'error',
+      {'groups': [['&&', '||']]}
+    ],
+    'no-unneeded-ternary': 'error',
     'no-prototype-builtins': 'off', // Allow using hasOwnProperty.
+    'max-len': [
+      'warn', 
+      100
+    ],
+    // Styling.
+    'yoda': 'error',
+    'no-multi-spaces': 'error',
+    'camelcase': 'warn',
+    'quotes': [
+      'error',
+      'single'
+    ],
+    'brace-style': [
+      'error', 
+      '1tbs',
+      {'allowSingleLine': true}
+    ],
+    'func-names': [
+      'error', 
+      'never'
+    ],
+    'indent': [
+      'error',
+      2,
+      {'SwitchCase': 1}
+    ],
+    'operator-assignment': 'error',
+    'no-tabs': 'error',
+    'comma-spacing': 'error',
+    'block-spacing': 'error',
+    'space-before-blocks': 'error',
+    'func-call-spacing': 'error',
+    'key-spacing': 'error',
+    'keyword-spacing': 'error',
+    'no-whitespace-before-property': 'error',
+    'space-infix-ops': 'error',
+    'semi-spacing': 'error',
+    'space-unary-ops': 'error',
+    'space-before-function-paren': ['error', {
+      'anonymous': 'never',
+      'named': 'never',
+      'asyncArrow': 'always',
+    }],
+    'computed-property-spacing': 'error',
+    'space-in-parens': 'error',
+    /*'array-bracket-spacing': [
+      'error', 
+      'never'
+    ],
+    'object-curly-spacing': 'error',*/
+
   }
 };

src/client/js/cell-info.js

@@ -143,21 +143,22 @@ class CellInfo {
     this.isClass[cell] = cell == cls;
 
     // Set cell classes.
-    cellClass[cls] = null;
     cellClass[cell] = cls;
     classMembers[cell] = [];
 
-    if (classMembers[cls] == null) {
+    if (classMembers[cls] === undefined) {
       classMembers[cls] = [];
     }
 
     classMembers[cls].push(cell);
   }
 
   // when this function is called:
-  //-  all body wall muscle class members annotated at zhen lab will have their class become the generic 'body wall muscles'
-  // class instead of BWM01, BWM02, etc. to make it compatible for comparison with the John White dataset
-  // all other legacy classes will have no class members to make it compatible for comparison
+  //-  all body wall muscle class members annotated at zhen lab will have their 
+  // class become the generic 'body wall muscles' class instead of BWM01, BWM02,
+  // etc. to make it compatible for comparison with the John White dataset
+  // all other legacy classes will have no class members to make it compatible 
+  // for comparison
   setToLegacy() {
     Object.entries(this.cellClassLegacy).forEach(entry => {
       let [cls, legacyCellClass] = entry;
@@ -173,7 +174,8 @@ class CellInfo {
   }
 
   // the inverse function of setToLegacy
-  // - zhen lab specific body wall muscle cells will revert to their correct class
+  // - zhen lab specific body wall muscle cells will revert to their correct 
+  // class
   // - legacy classes will have their class members registered again
   setToNonLegacy() {
     Object.entries(this.cellClassNonLegacy).forEach(entry => {

src/client/js/controller/index.js

@@ -420,7 +420,7 @@ class Controller extends EventEmitter {
     bindLegendEvents({ model, view });
   }
 
-  setState(state, fromUrl=false) {
+  setState(state, fromUrl = false) {
     let { model, view } = this;
 
     model.clear();
@@ -429,8 +429,8 @@ class Controller extends EventEmitter {
     let database = state['database'] || 'head';
     let allDatasets = DataService.getDatasetList(database);
     let datasets = intersection(allDatasets, state['datasets'] || []);
-    if (datasets.length == 0) {
-        datasets = database == 'head' ? ['witvliet_2020_7', 'witvliet_2020_8'] : allDatasets;
+    if (datasets.length === 0) {
+      datasets = (database == 'head') ? ['witvliet_2020_7', 'witvliet_2020_8'] : allDatasets;
     }
     let nodeColor = state['nodeColor'] || 'type';
     let layout = state['layout'] || 'concentric';

src/client/js/controller/tour.js

@@ -78,12 +78,12 @@ class Tour {
         this.view.help.hideTour();
         this.view.graph.one('layoutstop', () => d.resolve());
 
-        if (step.state != null) {
+        if (step.state !== undefined) {
           for (let key in step.state) {
             this.state[key] = step.state[key];
           }
 
-          if (step.state.coordinates != null) {
+          if (step.state.coordinates !== undefined) {
             this.state.coordinates = this.view.graph.scaleCoordinatesToViewport(
               deepCopy(this.state.coordinates)
             );

src/client/js/data-service.js

@@ -117,9 +117,9 @@ class DataService {
     )[0];
   }
 
-  getDatasetById(datasetId){
+  getDatasetById(datasetId) {
     this.checkLoaded();
-    return this.datasets.find( d => d.id === datasetId );
+    return this.datasets.find(d => d.id === datasetId);
   }
 
   setDatasetType(databaseType) {
@@ -194,7 +194,7 @@ class DataService {
       ANALDEP: 'anal dep'
     };
 
-    if (namesWithSpaces[name] != null) {
+    if (namesWithSpaces[name] !== undefined) {
       return namesWithSpaces[name];
     }
 

src/client/js/init.js

@@ -117,9 +117,9 @@ $(document).ready(() => {
       view.searchbar.focus();
     })
     .catch(e => {
-      let errorMsg =
-        'Cannot load data!\nPlease contact us if the problem persists!';
-      alert(errorMsg);
+      if (!DEBUG) {
+        alert('Cannot load data!\nPlease contact us if the problem persists!');
+      }
       throw e;
     });
 });

src/client/js/model/cytoscape-adaptor.js

@@ -170,9 +170,9 @@ ModelPrototype.makeCytoscapeEdge = function(
 
   // only add the first annotation type w.r.t annnotation order
   //that is found in this connections annotations
-  if (showAnnotations && this.database == 'head'){
+  if (showAnnotations && this.database == 'head') {
     let edgeIsAnnotated = false;
-    for ( let annotation of ANNOTATION_ORDER ){
+    for (let annotation of ANNOTATION_ORDER) {
       if (annotations.includes(annotation)) {
         classes.push(ANNOTATION_DISPLAY_LABEL_MAP[annotation]);
         edgeIsAnnotated = true;

src/client/js/model/groups.js

@@ -18,7 +18,7 @@ ModelPrototype.createGroup = function({
     return i + '';
   };
 
-  let groupId = id == null ? findValidGroupId() : id;
+  let groupId = (id === null || id === undefined) ? findValidGroupId() : id;
 
   this.groups[groupId] = {
     id: groupId,
@@ -91,15 +91,15 @@ ModelPrototype.getGroups = function() {
 };
 
 ModelPrototype.getGroupById = function(groupId) {
-  if (this.groups[groupId] == null) {
+  if (!this.groups.hasOwnProperty(groupId)) {
     throw new Error(`${groupId} is not a group`);
   }
 
   return this.groups[groupId];
 };
 
 ModelPrototype.getGroupByMemberId = function(groupMemberId) {
-  if (this.parent[groupMemberId] == null) {
+  if (!this.parent.hasOwnProperty(groupMemberId)) {
     throw new Error(`${groupMemberId} does not belong to a group`);
   }
 
@@ -141,11 +141,11 @@ ModelPrototype.positionGroupMembers = function(groupId) {
   let groupMemberXPositions = [];
   let groupMemberYPositions = [];
 
-  let groupMembersWithoutPositions = groupMembers.filter( m => {
+  let groupMembersWithoutPositions = groupMembers.filter(m => {
     let hasPosition = true;
     try {
       this.getPosition(m);
-    } catch (e){
+    } catch (e) {
       hasPosition = false;
     }
     return !hasPosition;
@@ -164,7 +164,7 @@ ModelPrototype.positionGroupMembers = function(groupId) {
 
   this.setPositions(gridPositions);
 
-  groupMembers.forEach( m => {
+  groupMembers.forEach(m => {
     let { x, y } = this.getPosition(m);
     groupMemberXPositions.push(x);
     groupMemberYPositions.push(y);
@@ -184,7 +184,7 @@ ModelPrototype.positionGroupMembers = function(groupId) {
 };
 
 ModelPrototype.group = function(nodes) {
-  let groupId = null;
+  let groupId;
   let toGroup = [];
 
   nodes.forEach(node => {
@@ -202,7 +202,7 @@ ModelPrototype.group = function(nodes) {
   }
 
   // Create group if no group is selected.
-  if (groupId == null) {
+  if (groupId === undefined) {
     groupId = this.createGroup();
     let meanPositionOfToGroup = meanPosition(
       toGroup.map(id => this.getPosition(id))
@@ -223,12 +223,12 @@ ModelPrototype.group = function(nodes) {
 };
 
 ModelPrototype.groupSelected = function() {
-  let groupId = null;
+  let groupId;
   if (this.canBeGrouped(this.getRawSelected())) {
     groupId = this.group(this.getRawSelected());
   }
 
-  if (groupId != null) {
+  if (groupId !== undefined) {
     this.setSelected([groupId]);
   }
 

src/client/js/model/index.js

@@ -1,13 +1,11 @@
-const modelToCytoscape = require('./cytoscape-adaptor');
-
 const EventEmitter = require('../EventEmitter');
-
 const services = require('../services');
 const DataService = require('../data-service');
 
-const { positionModule } = require('./position');
+const modelToCytoscape = require('./cytoscape-adaptor');
 const summary = require('./summary');
 const setters = require('./setters');
+const { positionModule } = require('./position');
 const splitJoin = require('./split-join');
 const input = require('./input');
 const hide = require('./hidden');
@@ -19,17 +17,6 @@ class Model extends EventEmitter {
   constructor(cy) {
     super();
     this.cy = cy;
-    //this.database; //eventually this and all following will be local variables.
-    //this.datasets;
-    //this.nodeColor;
-    //this.layout;
-    //this.showLinked;
-    //this.showIndividual;
-    //this.showEdgeLabel;
-    //this.showPostemb;
-    //this.thresholdChemical;
-    //this.thresholdElectrical;
-    //this.showAnnotations;
 
     this.legendItems = [];
 
@@ -41,7 +28,7 @@ class Model extends EventEmitter {
     this.joined = [];
 
     this.groups = {};
-    this.parent = {}; // should only be used by the groups module, every other module should not access this directly
+    this.parent = {}; // should only be used by the groups module, no other module should not access this directly
 
     this.positions = {};
     this.lockedPositions = [];
@@ -66,6 +53,7 @@ class Model extends EventEmitter {
     });
   }
 
+
   updateNetwork(updateType = '', runLayout = true) {
     this.emit('networkUpdate');
 

src/client/js/model/input.js

@@ -65,7 +65,7 @@ ModelPrototype.replaceClassMembersWithClassInInput = function(
   });
 };
 
-ModelPrototype.getValidInput = function(rawInput){
+ModelPrototype.getValidInput = function(rawInput) {
   return unique(rawInput).filter((nodeId, i, arr) => {
     let cellClass = DataService.cellClass(nodeId);
     let containsCellClass = arr.includes(cellClass);
@@ -76,14 +76,14 @@ ModelPrototype.getValidInput = function(rawInput){
 
 };
 
-ModelPrototype.setInputFromUrlState = function(rawInput){
+ModelPrototype.setInputFromUrlState = function(rawInput) {
 
   let validInput = this.getValidInput(rawInput);
   let previousValidInput = this.getValidInput(this.input);
   let newValidInput = difference(validInput, previousValidInput);
 
-  // Emit notification if input contains hidden post-embryonic nodes or nodes only present in
-  // other datasets.
+  // Emit notification if input contains hidden post-embryonic nodes or nodes 
+  // only present in other datasets.
   if (!this.showPostemb) {
     let newPostEmbInput = newValidInput
       .filter(nodeId => !DataService.isEmb(nodeId))
@@ -181,9 +181,9 @@ ModelPrototype.setInput = function(rawInput) {
   let validInput = this.getValidInput(rawInput);
 
   let groupIds = validInput
-  .filter(nodeId => this.isGroupMember(nodeId))
-  .map(nodeId => this.getGroupByMemberId(nodeId))
-  .map(group => group.id);
+    .filter(nodeId => this.isGroupMember(nodeId))
+    .map(nodeId => this.getGroupByMemberId(nodeId))
+    .map(group => group.id);
 
   this.unhide(validInput.concat(groupIds));
 

src/client/js/model/setters.js

@@ -61,7 +61,7 @@ ModelPrototype.setShowEdgeLabel = function(checked) {
   this.emit('showEdgeLabelChanged', checked);
 };
 
-ModelPrototype.setShowAnnotations = function(checked){
+ModelPrototype.setShowAnnotations = function(checked) {
   this.showAnnotations = checked;
   this.emit('showAnnotationsChanged', checked);
 };