lint fixes

frontend-js/.gitignore

 /dist/
 /coverage/
 /node_modules/
+/npm-debug.log

frontend-js/.jshintrc

@@ -24,6 +24,9 @@
     "smarttabs": true,
     
   "globals"   : {
+    
+    "alert" : false,
+
     /* MOCHA */
     "describe"   : false,
     "it"         : false,
@@ -37,9 +40,54 @@
     "ServerConnector"  : false,
     "google"  : false,
 
+    /* JSF commands */
+    "_actualizeParams"                  : false,
+    "_clearChemicalOverlayCollection"   : false,
+    "_clearCommentOverlayCollection"    : false,
+    "_clearDrugOverlayCollection"       : false,
+    "_clearMiRnaOverlayCollection"      : false,
+    "_clearMissingConnectionOverlayCollection" : false,
+    "_clearSearchOverlayCollection"     : false,
+    "_createSubmodelDialog"             : false,
+    "_refreshChemicalOverlayCollection" : false,
+    "_refreshCommentOverlayCollection"  : false,
+    "_refreshDrugOverlayCollection"     : false,
+    "_refreshMiRnaOverlayCollection"    : false,
+    "_refreshMissingConnectionOverlayCollection"    : false,
+    "_refreshSearchOverlayCollection"   : false,
+    "_requestChemicalDetailDataFunction": false,
+    "_requestCommentDetailDataFunction" : false,
+    "_requestDrugDetailDataFunction"    : false,
+    "_requestMiRnaDetailDataFunction"   : false,
+    "_registerChemicalOverlayCollection": false,
+    "_registerCommentOverlayCollection" : false,
+    "_registerDrugOverlayCollection"    : false,
+    "_registerMiRnaOverlayCollection"   : false,
+    "_registerMissingConnectionOverlayCollection"   : false,
+    "_registerSearchOverlayCollection"  : false,
+    "_retreiveActiveAliasesForLayout"   : false,
+    "_retreiveActiveReactionsForLayout" : false,
+    "_retreiveFullAliases"              : false,   
+    "_retreiveFullAliasesForLayout"     : false,
+    "_retreiveLightAliases"             : false,
+    "_retreiveLightReactions"           : false,
+    "_searchByCoord"                    : false,
+    "_sendReferenceGenomeDetailRequest" : false,
+    "_setShowComments"                  : false,
+    "_setModelZoomLevel"                : false,
+    "_searchMissingConnections"         : false,
+    "_updateCommentList"                : false,
+    
+    
+    
     /* jQuery */
     "$"  : false,
-    "jQuery"  : false
+    "jQuery"  : false,
+    
+    
+    /* Primefaces */
+    "PrimeFaces"    : false,
+    "PF"            : false
   }
     
 }

frontend-js/src/main/js/Configuration.js

@@ -27,10 +27,10 @@ function Configuration(data) {
 
   this.registerListenerType("onreload");
 
-  if (data != null) {
+  if (data !== undefined) {
     this.loadFromModelView(data);
   }
-};
+}
 
 // this class inherits from ObjectWithListeners class where generic methods for
 // listeners are set
@@ -48,7 +48,7 @@ Configuration.prototype.loadFromModelView = function(modelView) {
     // replace is due to some strange problem with serialization
     modelView = JSON.parse(modelView.replace(/\n/g, " "));
   }
-  this.ID_MODEL = modelView.idObject;
+  this.ID_MODEL = parseInt(modelView.idObject);
   this.TILE_SIZE = modelView.tileSize;
   this.PICTURE_SIZE = modelView.pictureSize;
   this.MAX_ZOOM = modelView.maxZoom;
@@ -61,7 +61,7 @@ Configuration.prototype.loadFromModelView = function(modelView) {
   this.MAPS = this.MAPS.concat(modelView.customLayouts);
 
   this.SUBMODELS = [];
-  if (modelView.submodels != null) {
+  if (modelView.submodels !== undefined) {
     for (var i = 0; i < modelView.submodels.length; i++) {
       var conf = new Configuration();
       conf.loadFromModelView(modelView.submodels[i]);

frontend-js/src/main/js/Functions.js

@@ -8,12 +8,12 @@ var Functions = {};
  * Bounds value between opt_min and opt_max (result will be not smaller than
  * opt_min and not bigger than opt_max).
  */
-Functions.bound = function(value, opt_min, opt_max) {
-  if (opt_min != null) {
-    value = Math.max(value, opt_min);
+Functions.bound = function(value, minVal, maxVal) {
+  if (minVal !== null && minVal !== undefined) {
+    value = Math.max(value, minVal);
   }
-  if (opt_max != null) {
-    value = Math.min(value, opt_max);
+  if (maxVal !== null && maxVal !== undefined) {
+    value = Math.min(value, maxVal);
   }
   return value;
 };
@@ -27,6 +27,7 @@ Functions.radiansToDegrees = function(rad) {
 };
 
 Functions.intToColorString = function(value) {
+  /* jslint bitwise: true */
   var timmedValue = (value & 0xFFFFFF);
   var colorStr = timmedValue.toString(16);
   while (colorStr.length < 6) {
@@ -89,7 +90,7 @@ Functions.pointInsidePolygon = function(point, polygon) {
   for (var i = 0, j = polygon.length - 1; i < polygon.length; j = i++) {
     var xi = polygon[i].x, yi = polygon[i].y;
     var xj = polygon[j].x, yj = polygon[j].y;
-    var intersect = ((yi > y) != (yj > y))
+    var intersect = ((yi > y) !== (yj > y))
         && (x < (xj - xi) * (y - yi) / (yj - yi) + xi);
     if (intersect) {
       inside = !inside;
@@ -112,20 +113,21 @@ Functions.browser = {
       // Get the user agent string
       var ua = navigator.userAgent;
       this.compatibilityMode = false;
-      if (navigator.appName == 'Microsoft Internet Explorer') {
+      var re;
+      if (navigator.appName === 'Microsoft Internet Explorer') {
         this.name = "IE";
-        var re = new RegExp("MSIE ([0-9]{1,}[\.0-9]{0,})");
-        if (re.exec(ua) != null) {
+        re = new RegExp("MSIE ([0-9]{1,}[\.0-9]{0,})");
+        if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
           this.version = parseFloat(RegExp.$1);
         }
         if (ua.indexOf("MSIE 7.0") > -1) {
           this.compatibilityMode = true;
         }
-      } else if (navigator.appName == 'Netscape') {
+      } else if (navigator.appName === 'Netscape') {
         this.name = "IE";
-        var ua = navigator.userAgent;
-        var re = new RegExp("Trident/.*rv:([0-9]{1,}[\.0-9]{0,})");
-        if (re.exec(ua) != null) {
+        ua = navigator.userAgent;
+        re = new RegExp("Trident/.*rv:([0-9]{1,}[\.0-9]{0,})");
+        if (re.exec(ua) !== undefined && re.exec(ua) !== null) {
           this.version = parseFloat(RegExp.$1);
         }
         if (ua.indexOf("MSIE 7.0") > -1) {
@@ -164,12 +166,15 @@ Functions.isDomElement = function(o) {
 };
 
 Functions.overlayToColor = function(elementOverlay) {
-  if (elementOverlay == null) {
+  /* jslint bitwise: true */
+  if (elementOverlay === null || elementOverlay === undefined) {
     logger.error("elementOverlay cannot be null!");
     return null;
-  } else if (elementOverlay.color != null) {
+  } else if (elementOverlay.color !== undefined
+      && elementOverlay.color !== null) {
     return this.intToColorString(elementOverlay.color.value);
-  } else if (elementOverlay.value != null) {
+  } else if (elementOverlay.value !== undefined
+      && elementOverlay.value !== null) {
     var ratio = 0;
     var color;
     if (elementOverlay.value < 0) {
@@ -194,7 +199,7 @@ Functions.overlayToColor = function(elementOverlay) {
     blue = parseInt(blue);
     blue = blue & 0x0000FF;
 
-    var color = red | green | blue;
+    color = red | green | blue;
     return this.intToColorString(color);
   } else {
     logger.error("elementOverlay doesn't have neither color nor value set!");

frontend-js/src/main/js/GuiConnector.js

 "use strict";
 
+var logger = require('./logger');
+
 var SearchPanel = require('./SearchPanel');
 var TabNavi = require('./TabNavi');
 
@@ -43,6 +45,17 @@ document.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function() {
   GuiConnector.getParams[decode(arguments[1])] = decode(arguments[2]);
 });
 
+GuiConnector.setCustomMap = function(customMap) {
+  if (customMap === undefined) {
+    logger.error("CustomMap cannot be undefiend");
+  }
+  this._customMap = customMap;
+};
+
+GuiConnector.getCustomMap = function() {
+  return this._customMap;
+};
+
 GuiConnector.init = function() {
   GuiConnector.leftPanelTabNavi = new TabNavi("tabView", {
     top : "17px"
@@ -57,7 +70,8 @@ GuiConnector.init = function() {
     tabSize : 1,
     top : "5px"
   });
-  if (document.getElementById("tabView:chemicalForm:chemicalResults") != null) {
+  if (document.getElementById("tabView:chemicalForm:chemicalResults") !== null
+      && document.getElementById("tabView:chemicalForm:chemicalResults") !== undefined) {
     GuiConnector.chemicalTabNavi = new TabNavi(
         "tabView:chemicalForm:chemicalResults", {
           hideRemaining : false,
@@ -74,7 +88,7 @@ GuiConnector.init = function() {
   GuiConnector.searchPanel = new SearchPanel(document
       .getElementById('tabView:mainForm:searchText_input'), document
       .getElementById('tabView:mainForm:searchButton'), function() {
-    tabViewVar.select(0);
+    _tabViewVar.select(0);
   });
 
 };
@@ -269,23 +283,24 @@ GuiConnector.getJsPopupForSubmodelId = function(id) {
  */
 GuiConnector.openDialog = function(id) {
   var jsVar = GuiConnector.getJsPopupForSubmodelId(id);
-  if (jsVar != null) {
+  if (jsVar !== null) {
     var htmlTag = GuiConnector.getHtmlTagForSubmodelId(id);
-    customMap.openSubmodel(id, htmlTag, jsVar);
+    this.getCustomMap().openSubmodel(id, htmlTag, jsVar);
   }
   return false;
 };
 
 GuiConnector.referenceToHtml = function(reference) {
-  if (reference.summary != null && reference.summary != "") {
-    var result = '<div title="' + reference.summary + '">';
+  var result;
+  if (reference.summary !== undefined && reference.summary !== "") {
+    result = '<div title="' + reference.summary + '">';
     result += '<a href="' + reference.link + '" target="_blank">'
         + reference.name + "</a>";
     // + reference.name + "(" + reference.type + ")</a>";
     result += "</div>";
     return result;
   } else {
-    var result = '<div><a href="' + reference.link + '" target="_blank">'
+    result = '<div><a href="' + reference.link + '" target="_blank">'
         + reference.name + "</a></div>";
     // + reference.name + "(" + reference.type + ")</a></div>";
     return result;
@@ -314,4 +329,8 @@ GuiConnector.getObjectByPrimefaceId = function(id) {
   return $(PrimeFaces.escapeClientId(id));
 };
 
+GuiConnector.getOverviewDialog = function() {
+  return _overviewDialog;
+};
+
 module.exports = GuiConnector;

frontend-js/src/main/js/ObjectWithListeners.js

@@ -9,7 +9,7 @@ var logger = require('./logger');
 function ObjectWithListeners() {
   this._validListeners = [];
   this._validPropertyListeners = [];
-};
+}
 
 /**
  * Adds a listener function to the object.
@@ -20,11 +20,11 @@ function ObjectWithListeners() {
  *            function that should be thrown when type event occures
  */
 ObjectWithListeners.prototype.addListener = function(type, fun) {
-  if (this._validListeners[type] == null) {
+  if (this._validListeners[type] === undefined) {
     throw "Unknown listener type: " + type;
   }
 
-  if (typeof (fun) != "function") {
+  if (typeof fun !== "function") {
     throw "Second parameter must be a function but \"" + typeof (fun)
         + "\" found.";
   }
@@ -42,11 +42,11 @@ ObjectWithListeners.prototype.addListener = function(type, fun) {
  *            called
  */
 ObjectWithListeners.prototype.addPropertyChangeListener = function(name, fun) {
-  if (this._validPropertyListeners[name] == null) {
+  if (this._validPropertyListeners[name] === undefined) {
     throw "Unknown property type: " + name;
   }
 
-  if (typeof (fun) != "function") {
+  if (typeof fun !== "function") {
     throw "Second parameter must be a function but \"" + typeof (fun)
         + "\" found.";
   }
@@ -61,7 +61,7 @@ ObjectWithListeners.prototype.addPropertyChangeListener = function(name, fun) {
  *            string identifing new type of listener
  */
 ObjectWithListeners.prototype.registerListenerType = function(type) {
-  if (this._validListeners[type] != null) {
+  if (this._validListeners[type] !== undefined) {
     throw "Listener type already registered: " + type;
   }
   this._validListeners[type] = [];
@@ -74,7 +74,7 @@ ObjectWithListeners.prototype.registerListenerType = function(type) {
  *            string identifing proeprty
  */
 ObjectWithListeners.prototype.registerPropertyType = function(name) {
-  if (this._validPropertyListeners[name] != null) {
+  if (this._validPropertyListeners[name] !== undefined) {
     throw "Property already registered: " + name;
   }
   this._validPropertyListeners[name] = [];
@@ -89,11 +89,11 @@ ObjectWithListeners.prototype.registerPropertyType = function(name) {
  *            function that was call when event occred that should be removed
  */
 ObjectWithListeners.prototype.removeListener = function(type, fun) {
-  if (this._validListeners[type] == null) {
+  if (this._validListeners[type] === undefined) {
     throw "Unknown listener type: " + type;
   }
 
-  if (typeof (fun) != "function") {
+  if (typeof (fun) !== "function") {
     throw "Second parameter must be a function but \"" + typeof (fun)
         + "\" found.";
   }
@@ -117,11 +117,11 @@ ObjectWithListeners.prototype.removeListener = function(type, fun) {
  *            function that was call when event occred that should be removed
  */
 ObjectWithListeners.prototype.removePropertyListener = function(name, fun) {
-  if (this._validPropertyListeners[name] == null) {
+  if (this._validPropertyListeners[name] === undefined) {
     throw "Unknown property: " + name;
   }
 
-  if (typeof (fun) != "function") {
+  if (typeof (fun) !== "function") {
     throw "Second parameter must be a function but \"" + typeof (fun)
         + "\" found.";
   }
@@ -143,7 +143,7 @@ ObjectWithListeners.prototype.removePropertyListener = function(name, fun) {
  *            type of the listener (string)
  */
 ObjectWithListeners.prototype.callListeners = function(type) {
-  if (this._validListeners[type] == null) {
+  if (this._validListeners[type] === undefined) {
     throw "Unknown listener type: " + type;
   }
   var listenerList = this._validListeners[type];
@@ -171,7 +171,7 @@ ObjectWithListeners.prototype.callListeners = function(type) {
 ObjectWithListeners.prototype.firePropertyChangeListener = function(
     propertyName, oldval, newval) {
   var self = this;
-  if (this._validPropertyListeners[propertyName] == null) {
+  if (this._validPropertyListeners[propertyName] === undefined) {
     throw "Unknown property type: " + propertyName;
   }
   var listenerList = this._validPropertyListeners[propertyName];

frontend-js/src/main/js/ServerConnector.js

@@ -145,8 +145,12 @@ ServerConnector.setVisibleLayouts = function(value) {
  * Get layout of the {@link CustomMap} which was last browsed.
  */
 ServerConnector.getSelectedLayout = function() {
-  return document.getElementById(ServerConnector.formIdentifier
+  var result = document.getElementById(ServerConnector.formIdentifier
       + ':selectedLayout').value;
+  if (result === undefined) {
+    result = null;
+  }
+  return result;
 };
 
 /**
@@ -171,7 +175,7 @@ ServerConnector.actualizeSessionData = function() {
  * @see ServerConnector.actualizeSessionData
  */
 ServerConnector.actualizeParams = function() {
-  actualizeParams();
+  _actualizeParams();
 };
 
 /**
@@ -243,7 +247,7 @@ ServerConnector.setShowComments = function(value) {
 ServerConnector.showSimilarDataMining = function(param) {
   document.getElementById(ServerConnector.formIdentifier + ':geneName').value = ""
       + param;
-  searchMissingConnections();
+  _searchMissingConnections();
 };
 
 /**
@@ -345,9 +349,9 @@ ServerConnector.retreiveLightReactions = function(ids) {
  */
 ServerConnector.sendRefreshRequest = function(overlayName) {
   var functions = ServerConnector._overlayMethods[overlayName];
-  if (functions != null) {
+  if (functions !== undefined) {
     var refreshFunction = functions.refreshFunction;
-    if (refreshFunction != null) {
+    if (refreshFunction !== undefined) {
       refreshFunction();
     } else {
       logger.warn("Refresh function for " + overlayName + " doesn't exist");
@@ -361,13 +365,13 @@ ServerConnector.sendRefreshRequest = function(overlayName) {
  * Adds {@link OverlayCollection} to ServerConnector.
  */
 ServerConnector.addOverlayCollection = function(overlay) {
-  if (ServerConnector._overlayMethods[overlay.name] != null) {
-    if (ServerConnector._overlays[overlay.name] != null) {
+  if (ServerConnector._overlayMethods[overlay.name] !== undefined) {
+    if (ServerConnector._overlays[overlay.name] !== undefined) {
       logger.warn("Overlay with name " + overlay.name + " already added");
       return;
     }
     ServerConnector._overlays[overlay.name] = overlay;
-    if (ServerConnector._overlayMethods[overlay.name].initFunction != null) {
+    if (ServerConnector._overlayMethods[overlay.name].initFunction !== undefined) {
       ServerConnector._overlayMethods[overlay.name].initFunction();
     } else {
       logger.warn("Cannot initialize overlay: " + overlay);
@@ -390,7 +394,7 @@ ServerConnector.addOverlayCollection = function(overlay) {
 ServerConnector.updateOverlayCollection = function(overlayName, data, fitBounds) {
   logger.debug("Updating: " + overlayName);
   var overlay = ServerConnector._overlays[overlayName];
-  if (overlay != null) {
+  if (overlay !== undefined) {
     overlay.updateOverlays(data, fitBounds);
   } else {
     logger.warn("Overlay " + overlayName
@@ -699,9 +703,9 @@ ServerConnector._overlayMethods[ServerConnector.MI_RNA_OVERLAY_NAME] = {
 
 ServerConnector.sendClearRequest = function(overlayName) {
   var functions = ServerConnector._overlayMethods[overlayName];
-  if (functions != null) {
+  if (functions !== undefined) {
     var clearFunction = functions.clearFunction;
-    if (clearFunction != null) {
+    if (clearFunction !== undefined) {
       clearFunction();
     } else {
       logger.warn("Clear function for " + overlayName + " doesn't exist");
@@ -713,7 +717,7 @@ ServerConnector.sendClearRequest = function(overlayName) {
 
 ServerConnector.setOverlayResultIds = function(overlayName, ids) {
   var overlay = this._overlays[overlayName];
-  if (overlay != null) {
+  if (overlay !== undefined) {
     overlay.setResultsIds(ids);
   } else {
     logger.warn("Overlay '" + overlayName + "' doesn't exist");
@@ -723,17 +727,17 @@ ServerConnector.setOverlayResultIds = function(overlayName, ids) {
 ServerConnector.sendOverlayDetailDataRequest = function(overlayName,
     identifiedElement, general) {
   var overlay = ServerConnector._overlays[overlayName];
-  if (overlay == null) {
+  if (overlay === undefined) {
     logger.warn("Unknown overlay: " + overlayName);
     return;
   }
   var functions = ServerConnector._overlayMethods[overlayName];
-  if (functions != null) {
+  if (functions !== undefined) {
     var requestDetailDataFunction = functions.requestDetailDataFunction;
-    if (requestDetailDataFunction != null) {
+    if (requestDetailDataFunction !== undefined) {
       var missingData = overlay.getMissingDetailDataIds(identifiedElement,
           general);
-      if (missingData.length == 0) {
+      if (missingData.length === 0) {
         logger
             .warn(
                 "request of missing data called for empty data set... overlay name = ",
@@ -755,7 +759,7 @@ ServerConnector.sendOverlayDetailDataRequest = function(overlayName,
 ServerConnector.updateOverviewElementDetailData = function(overlayName,
     searchResultIdentifier, identifiedElement, data) {
   var overlay = this._overlays[overlayName];
-  if (overlay != null) {
+  if (overlay !== undefined) {
     overlay.updateOverviewElementDetailData(identifiedElement,
         searchResultIdentifier, data);
   } else {
@@ -771,10 +775,10 @@ ServerConnector.updateOverviewElementDetailData = function(overlayName,
  *          data from server, <code>false</code> otherwise.
  */
 ServerConnector.isWaitingForData = function() {
-  var result = (this._waitingForAliasLayoutData != 0) || //
-  (this._waitingForAliasData != 0) || //
-  (this._waitingForReactionLayoutData != 0) || //
-  (this._waitingForReactionData != 0);
+  var result = (this._waitingForAliasLayoutData !== 0) || //
+  (this._waitingForAliasData !== 0) || //
+  (this._waitingForReactionLayoutData !== 0) || //
+  (this._waitingForReactionData !== 0);
   return result;
 };
 
@@ -808,7 +812,7 @@ ServerConnector.setWaitingForAliasLayoutData = function(layoutId, value) {
         "WaitingForAliasLayoutData layoutId must be integer, but found: ",
         layoutId);
   }
-}
+};
 
 ServerConnector.setWaitingForFullAliasLayoutData = function(layoutId, aliasId,
     value) {
@@ -840,7 +844,7 @@ ServerConnector.setWaitingForFullAliasLayoutData = function(layoutId, aliasId,
         "setWaitingForFullAliasLayoutData value must be boolean, but found: ",
         value);
   }
-}
+};
 
 ServerConnector.isWaitingForFullAliasLayoutData = function(layoutId, aliasId) {
   if (!functions.isInt(layoutId)) {
@@ -856,11 +860,11 @@ ServerConnector.isWaitingForFullAliasLayoutData = function(layoutId, aliasId) {
   }
 
   var val = this._waitingFullAliasLayoutDataById[layoutId + "-" + aliasId];
-  if (val == null) {
+  if (val === undefined) {
     return false;
   }
   return val;
-}
+};
 
 /**
  * Sets waitingForAliasData flag that monitors if we are waiting for the data
@@ -1036,22 +1040,41 @@ ServerConnector.updateReferenceGenomeData = function(organismId, type, version,
 
 ServerConnector.getMinOverlayColorInt = function() {
   var color = document.getElementById("overlayConfigForm:userMinColor").value;
-  if (color == "") {
+  if (color === "") {
     color = document.getElementById("overlayConfigForm:systemMinColor").value;
   }
   color = parseInt(color, 16);
-  var color = (color & 0xFFFFFF);
+  /* jslint bitwise: true */
+  color = (color & 0xFFFFFF);
   return color;
 };
 
 ServerConnector.getMaxOverlayColorInt = function() {
   var color = document.getElementById("overlayConfigForm:userMaxColor").value;
-  if (color == "") {
+  if (color === "") {
     color = document.getElementById("overlayConfigForm:systemMaxColor").value;
   }
   color = parseInt(color, 16);
-  var color = (color & 0xFFFFFF);
+  /* jslint bitwise: true */
+  color = (color & 0xFFFFFF);
   return color;
 };
 
+ServerConnector.createSubmodelDialog = function(submodelId) {
+  _createSubmodelDialog([ {
+    name : 'submodelId',
+    value : submodelId
+  } ]);
+};
+
+ServerConnector.setModelZoomLevel = function(id, zoom) {
+  _setModelZoomLevel([ {
+    name : 'mapId',
+    value : id
+  }, {
+    name : 'zoomLevel',
+    value : zoom
+  } ]);
+};
+
 module.exports = ServerConnector;

frontend-js/src/main/js/TabNavi.js

 "use strict";
 
+var logger = require('./logger');
+
 /**
  * Class that adds tab navigation to defavult primefaces tabView component.
  */
 function TabNavi(elementId, params) {
   var self = this;
 
-  if (params == null) {
+  if (params === undefined) {
     params = {};
   }