Merge branch 'small-refactor' into 'master'

Small refactor

See merge request piotr.gawron/minerva!177

frontend-js/src/main/js/map/data/Alias.js

@@ -2,6 +2,7 @@
 
 var BioEntity = require("./BioEntity");
 
+// noinspection JSUnusedLocalSymbols
 var logger = require('../../logger');
 
 /**
@@ -26,7 +27,7 @@ function Alias(javaObject) {
   }
 
   if (this._modelId === undefined) {
-    throw new Error("ModelId is not defined for alias", javaObject);
+    throw new Error("ModelId is not defined for alias");
   }
 
   if (javaObject.name === undefined) {

frontend-js/src/main/js/map/marker/AliasMarker.js

@@ -40,8 +40,8 @@ AliasMarker.prototype.setAliasData = function (data) {
  * @returns {google.maps.Point} - coordinates where marker is pointing
  */
 AliasMarker.prototype.getCoordinates = function () {
-  return new google.maps.Point(this._aliasData.x + this._aliasData.width / 2, this._aliasData.y
-    + this._aliasData.height / 2);
+  var alias = this.getAliasData();
+  return new google.maps.Point(alias.getX() + alias.getWidth() / 2, alias.getY() + alias.getHeight() / 2);
 };
 
 AliasMarker.prototype.init = function () {

frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js

@@ -8,7 +8,7 @@ var ObjectWithListeners = require('../../ObjectWithListeners');
  * Class representing abstract overlay element on the map relevant for a
  * specific layout.
  */
-function AbstractOverlayElement(params) {
+function AbstractSurfaceElement(params) {
   var self = this;
   // call super constructor
   ObjectWithListeners.call(this);
@@ -31,16 +31,16 @@ function AbstractOverlayElement(params) {
   }
 }
 
-AbstractOverlayElement.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractOverlayElement.prototype.constructor = AbstractOverlayElement;
+AbstractSurfaceElement.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractSurfaceElement.prototype.constructor = AbstractSurfaceElement;
 
-AbstractOverlayElement.prototype.setMap = function(map) {
+AbstractSurfaceElement.prototype.setMap = function (map) {
   for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
     this.getGoogleMapObjects()[i].setMap(map);
   }
 };
 
-AbstractOverlayElement.prototype.getBounds = function() {
+AbstractSurfaceElement.prototype.getBounds = function () {
   var bounds = new google.maps.LatLngBounds();
   for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
     bounds.extend(this.getGoogleMapObjects()[i].getBounds().getSouthWest());
@@ -49,7 +49,7 @@ AbstractOverlayElement.prototype.getBounds = function() {
   return bounds;
 };
 
-AbstractOverlayElement.prototype.isShown = function() {
+AbstractSurfaceElement.prototype.isShown = function () {
   var result = false;
   for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
     var map = this.getGoogleMapObjects()[i].getMap();
@@ -61,7 +61,7 @@ AbstractOverlayElement.prototype.isShown = function() {
   return result;
 };
 
-AbstractOverlayElement.prototype.show = function() {
+AbstractSurfaceElement.prototype.show = function () {
   if (this.isShown()) {
     logger.warn("Surface already shown");
     return;
@@ -69,51 +69,60 @@ AbstractOverlayElement.prototype.show = function() {
   this.setMap(this.getCustomMap().getGoogleMap());
 };
 
-AbstractOverlayElement.prototype.hide = function() {
+AbstractSurfaceElement.prototype.hide = function () {
   this.setMap(null);
 };
 
-AbstractOverlayElement.prototype.onClickHandler = function() {
+AbstractSurfaceElement.prototype.onClickHandler = function () {
   return this.callListeners("onClick");
 };
 
-AbstractOverlayElement.prototype.getGoogleMarker = function() {
+AbstractSurfaceElement.prototype.getGoogleMarker = function () {
   return this.getGoogleMapObjects()[0];
 };
 
-AbstractOverlayElement.prototype.getGoogleMapObjects = function() {
+AbstractSurfaceElement.prototype.getGoogleMapObjects = function () {
   return this._googleMapObjects;
 };
 
-AbstractOverlayElement.prototype.addGoogleMapObject = function(googleObject) {
+AbstractSurfaceElement.prototype.addGoogleMapObject = function (googleObject) {
   this._googleMapObjects.push(googleObject);
 
   var self = this;
-  var onclick = function() {
+  var onclick = function () {
     return self.onClickHandler();
   };
   google.maps.event.addListener(googleObject, 'click', onclick);
 };
 
-AbstractOverlayElement.prototype.getIdentifiedElement = function() {
+AbstractSurfaceElement.prototype.getIdentifiedElement = function () {
   return this._identifiedElement;
 };
 
-AbstractOverlayElement.prototype.getModelId = function() {
+AbstractSurfaceElement.prototype.setIdentifiedElement = function (identifiedElement) {
+  this._identifiedElement = identifiedElement;
+};
+
+AbstractSurfaceElement.prototype.getBioEntity = function () {
+  return this._bioEntity;
+};
+
+AbstractSurfaceElement.prototype.setBioEntity = function (bioEntity) {
+  this._bioEntity = bioEntity;
+};
+
+
+AbstractSurfaceElement.prototype.getModelId = function () {
   return this.getIdentifiedElement().getModelId();
 };
 
-AbstractOverlayElement.prototype.updateIdentifiedElement = function(identifiedElement) {
+AbstractSurfaceElement.prototype.updateIdentifiedElement = function (identifiedElement) {
   if (identifiedElement.getColor() !== undefined) {
     this.setColor(identifiedElement.getColor());
   }
 };
 
-AbstractOverlayElement.prototype.setIdentifiedElement = function(identifiedElement) {
-  this._identifiedElement = identifiedElement;
-};
-
-AbstractOverlayElement.prototype.getBounds = function() {
+AbstractSurfaceElement.prototype.getBounds = function () {
   var self = this;
   var bounds = new google.maps.LatLngBounds();
   for (var i = 0; i < self.getGoogleMapObjects().length; i++) {
@@ -127,15 +136,15 @@ AbstractOverlayElement.prototype.getBounds = function() {
 
 /**
  * Returns {@link AbstractCustomMap} where surface is located.
- * 
- * @returns {@link AbstractCustomMap} where surface is located
+ *
+ * @returns {AbstractCustomMap} where surface is located
  */
-AbstractOverlayElement.prototype.getCustomMap = function() {
+AbstractSurfaceElement.prototype.getCustomMap = function () {
   return this._customMap;
 };
 
-AbstractOverlayElement.prototype.setCustomMap = function(customMap) {
+AbstractSurfaceElement.prototype.setCustomMap = function (customMap) {
   this._customMap = customMap;
 };
 
-module.exports = AbstractOverlayElement;
+module.exports = AbstractSurfaceElement;

frontend-js/src/main/js/map/surface/AliasSurface.js

@@ -2,6 +2,7 @@
 
 /* exported logger */
 
+// noinspection JSUnusedLocalSymbols
 var logger = require('../../logger');
 var functions = require('../../Functions');
 
@@ -20,18 +21,18 @@ function AliasSurface(params) {
   this.addGoogleMapObject(params.gmapObj);
 
   // original data
-  this.aliasData = params.alias;
+  this.setBioEntity(params.alias);
 }
 
 AliasSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
 AliasSurface.prototype.constructor = AliasSurface;
 
-AliasSurface.prototype.setColor = function(color) {
+AliasSurface.prototype.setColor = function (color) {
   this._color = color;
   var googleMapObjects = this.getGoogleMapObjects();
   for (var i = 0; i < googleMapObjects.length; i++) {
     googleMapObjects[i].setOptions({
-      strokeColor : color,
+      strokeColor: color
     });
   }
 };
@@ -40,16 +41,16 @@ AliasSurface.prototype.setColor = function(color) {
  * Function used to recalculate boundaries of the {@link AliasSurface}.
  * Boundaries define how big part of original alias is taken by this layout
  * visualization.
- * 
+ *
  * @param startX
  *          value between 0..1 defining where should be the start on OX axis
  * @param endX
  *          value between 0..1 defining where should be the end on OX axis
  */
-AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
-  var pointA = new google.maps.Point(this.aliasData.x + startX * this.aliasData.width, this.aliasData.y);
-  var pointB = new google.maps.Point(this.aliasData.x + endX * this.aliasData.width, this.aliasData.y
-      + this.aliasData.height);
+AliasSurface.prototype.setBoundsForAlias = function (startX, endX) {
+  var alias = this.getBioEntity();
+  var pointA = new google.maps.Point(alias.x + startX * alias.width, alias.y);
+  var pointB = new google.maps.Point(alias.x + endX * alias.width, alias.y + alias.height);
   var latLngA = this.getCustomMap().fromPointToLatLng(pointA);
   var latLngB = this.getCustomMap().fromPointToLatLng(pointB);
 
@@ -61,7 +62,7 @@ AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
 
 /**
  * Creates {@link AliasSurface}.
- * 
+ *
  * @param params
  *          dict containing set of information required for surface creation:
  *          <li>overlayAlias - {@link LayoutAlias} for which overlay is created
@@ -79,7 +80,7 @@ AliasSurface.prototype.setBoundsForAlias = function(startX, endX) {
  *          starting point of the overlay
  * @returns {AliasSurface}
  */
-AliasSurface.create = function(params) {
+AliasSurface.create = function (params) {
   var overlayAlias = params.overlayAlias;
   var alias = params.alias;
   var map = params.map;
@@ -95,32 +96,32 @@ AliasSurface.create = function(params) {
   bounds.extend(latLngA);
   bounds.extend(latLngB);
   var rectangle = new google.maps.Rectangle({
-    fillOpacity : 0.8,
-    strokeWeight : 1,
-    map : map.getGoogleMap(),
-    bounds : bounds
+    fillOpacity: 0.8,
+    strokeWeight: 1,
+    map: map.getGoogleMap(),
+    bounds: bounds
   });
 
-  return functions.overlayToColor(overlayAlias).then(function(color) {
+  return functions.overlayToColor(overlayAlias).then(function (color) {
     rectangle.setOptions({
-      fillColor : color,
+      fillColor: color
     });
     var result = new AliasSurface({
-      map : map,
-      gmapObj : rectangle,
-      alias : alias,
-      onClick : params.onClick
+      map: map,
+      gmapObj: rectangle,
+      alias: alias,
+      onClick: params.onClick
     });
     result.setIdentifiedElement(new IdentifiedElement(alias));
     return result;
   });
 };
 
-AliasSurface.createFromIdentifiedElement = function(params) {
+AliasSurface.createFromIdentifiedElement = function (params) {
   var element = params.element;
   var map = params.map;
   var model = map.getModel().getSubmodelById(element.getModelId());
-  return model.getByIdentifiedElement(element).then(function(alias) {
+  return model.getByIdentifiedElement(element).then(function (alias) {
     var pointA = new google.maps.Point(alias.getX(), alias.getY());
     var pointB = new google.maps.Point(alias.getX() + alias.getWidth(), alias.getY() + alias.getHeight());
     var latLngA = map.fromPointToLatLng(pointA);
@@ -152,21 +153,21 @@ AliasSurface.createFromIdentifiedElement = function(params) {
     }
 
     var rectangle = new google.maps.Rectangle({
-      map : map.getGoogleMap(),
-      bounds : bounds,
-
-      fillOpacity : fillOpacity,
-      fillColor : color,
-      strokeColor : strokeColor,
-      strokeOpacity : strokeOpacity,
-      strokeWeight : strokeWeight,
+      map: map.getGoogleMap(),
+      bounds: bounds,
+
+      fillOpacity: fillOpacity,
+      fillColor: color,
+      strokeColor: strokeColor,
+      strokeOpacity: strokeOpacity,
+      strokeWeight: strokeWeight
     });
 
     var result = new AliasSurface({
-      gmapObj : rectangle,
-      map : map,
-      onClick : params.onClick,
-      alias : alias,
+      gmapObj: rectangle,
+      map: map,
+      onClick: params.onClick,
+      alias: alias
     });
     result.setIdentifiedElement(element);
     return result;

frontend-js/src/main/js/map/surface/ReactionSurface.js

 "use strict";
 
+var Promise = require("bluebird");
+
 /* exported logger */
 
 var functions = require('../../Functions');
@@ -29,7 +31,7 @@ function ReactionSurface(params) {
   AbstractSurfaceElement.call(this, params);
 
   var overlayData = params.layoutReaction;
-  this.setReactionData(params.reaction);
+  this.setBioEntity(params.reaction);
 
   var color = params.color;
   this.width = 5.0;
@@ -46,7 +48,7 @@ function ReactionSurface(params) {
 
   this.setColor(color);
   this.setCustomized(params.customized);
-  this.setIdentifiedElement(new IdentifiedElement(this.getReactionData()));
+  this.setIdentifiedElement(new IdentifiedElement(this.getBioEntity()));
 
   this.init();
 }
@@ -89,7 +91,7 @@ ReactionSurface.prototype.setColor = function (color) {
   var gmapObjects = this.getGoogleMapObjects();
   for (var i = 0; i < gmapObjects.length; i++) {
     gmapObjects[i].setOptions({
-      strokeColor: color,
+      strokeColor: color
     });
   }
   this.customized = true;
@@ -165,7 +167,7 @@ ReactionSurface.prototype.changedToDefault = function () {
   for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
     this.getGoogleMapObjects()[i].setOptions({
       strokeColor: "#0000FF",
-      strokeWeight: 5,
+      strokeWeight: 5
     });
   }
   this.customized = false;
@@ -175,11 +177,11 @@ ReactionSurface.prototype.changedToDefault = function () {
  * Changes visualization of the ReactionSurface to customized mode where we mark
  * reaction as highlighted with customized reaction layout data.
  */
-ReactionSurface.prototype.changedToCustomized = function() {
+ReactionSurface.prototype.changedToCustomized = function () {
   for (var i = 0; i < this.getGoogleMapObjects().length; i++) {
     this.getGoogleMapObjects()[i].setOptions({
       strokeColor: this.getColor(),
-      strokeWeight: this.getWidth(),
+      strokeWeight: this.getWidth()
     });
   }
   this.customized = true;
@@ -215,15 +217,6 @@ ReactionSurface.createLine = function (line, color, width, map) {
   return googleLine;
 };
 
-/**
- * Returns {@link Reaction} data for this marker.
- *
- * @returns {@link Reaction} data for this marker
- */
-ReactionSurface.prototype.getReactionData = function () {
-  return this.reactionData;
-};
-
 ReactionSurface.prototype.getId = function () {
   return this._id;
 };
@@ -232,11 +225,11 @@ ReactionSurface.prototype.setId = function (id) {
   this._id = id;
 };
 
-ReactionSurface.prototype.setReactionData = function (value) {
+ReactionSurface.prototype.setBioEntity = function (value) {
   if (value === undefined || value === null) {
     throw new Error("Reaction must be defined");
   }
-  this.reactionData = value;
+  AbstractSurfaceElement.prototype.setBioEntity.call(this, value);
   this.setId(value.getId());
 };
 
@@ -245,21 +238,22 @@ ReactionSurface.prototype.isCustomized = function () {
 };
 
 ReactionSurface.prototype.init = function () {
+  var reaction = this.getBioEntity();
   var i;
   var line;
   var googleLine;
-  for (i = 0; i < this.reactionData.startLines.length; i++) {
-    line = this.reactionData.startLines[i];
+  for (i = 0; i < reaction.startLines.length; i++) {
+    line = reaction.startLines[i];
     googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
     this.addGoogleMapObject(googleLine);
   }
-  for (i = 0; i < this.reactionData.endLines.length; i++) {
-    line = this.reactionData.endLines[i];
+  for (i = 0; i < reaction.endLines.length; i++) {
+    line = reaction.endLines[i];
     googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
     this.addGoogleMapObject(googleLine);
   }
-  for (i = 0; i < this.reactionData.midLines.length; i++) {
-    line = this.reactionData.midLines[i];
+  for (i = 0; i < reaction.midLines.length; i++) {
+    line = reaction.midLines[i];
     googleLine = ReactionSurface.createLine(line, this.getColor(), this.width, this.getCustomMap());
     this.addGoogleMapObject(googleLine);
   }

frontend-js/src/test/js/map/data/Alias-test.js

@@ -61,70 +61,91 @@ describe('Alias', function () {
   });
 
 
-  it("Alias update method", function () {
-    var javaObject = {
-      bounds: {
-        x: 190,
-        y: 44,
-        width: 80,
-        height: 40
-      },
-      modelId: 57,
-      idObject: 18554
-    };
-    var alias = new Alias(javaObject);
-    var javaObject2 = {
-      notes: "",
-      type: "Protein",
-      name: "s1",
-      synonyms: [],
-      formerSymbols: [],
-      references: [],
-      other: [],
-      bounds: {
-        x: 59,
-        y: 73,
-        width: 80,
-        height: 40
-      },
-      modelId: 54,
-      idObject: 18552
-    };
-    alias.update(javaObject2);
-    assert.ok(alias.isComplete());
-    assert.equal('s1', alias.name);
-  });
+  describe("update", function () {
+    describe("from json", function () {
+      it("full update", function () {
+        var javaObject = {
+          bounds: {
+            x: 190,
+            y: 44,
+            width: 80,
+            height: 40
+          },
+          modelId: 57,
+          idObject: 18554
+        };
+        var alias = new Alias(javaObject);
+        var javaObject2 = {
+          notes: "",
+          type: "Protein",
+          name: "s1",
+          synonyms: [],
+          formerSymbols: [],
+          references: [],
+          other: [],
+          bounds: {
+            x: 59,
+            y: 73,
+            width: 80,
+            height: 40
+          },
+          modelId: 54,
+          idObject: 18552
+        };
+        alias.update(javaObject2);
+        assert.ok(alias.isComplete());
+        assert.equal('s1', alias.getName());
+      });
+
+      it("partial update", function () {
+        var javaObject = {
+          bounds: {
+            x: 190,
+            y: 44,
+            width: 80,
+            height: 40
+          },
+          modelId: 57,
+          idObject: 18554
+        };
+        var alias = new Alias(javaObject);
+        var javaObject2 = {
+          notes: "",
+          type: "Protein",
+          synonyms: [],
+          formerSymbols: [],
+          references: [],
+          other: [],
+          bounds: {
+            x: 59,
+            y: 73,
+            width: 80,
+            height: 40
+          },
+          modelId: 54,
+          idObject: 18552
+        };
+        alias.update(javaObject2);
+        assert.equal(alias.isComplete(), false);
+      });
+    });
 
-  it("Alias update method 2", function () {
-    var javaObject = {
-      bounds: {
-        x: 190,
-        y: 44,
-        width: 80,
-        height: 40
-      },
-      modelId: 57,
-      idObject: 18554
-    };
-    var alias = new Alias(javaObject);
-    var javaObject2 = {
-      notes: "",
-      type: "Protein",
-      synonyms: [],
-      formerSymbols: [],
-      references: [],
-      other: [],
-      bounds: {
-        x: 59,
-        y: 73,
-        width: 80,
-        height: 40
-      },
-      modelId: 54,
-      idObject: 18552
-    };
-    alias.update(javaObject2);
-    assert.equal(alias.isComplete(), false);
+    it("from Alias", function () {
+      var javaObject = {
+        bounds: {
+          x: 190,
+          y: 44,
+          width: 80,
+          height: 40
+        },
+        modelId: 57,
+        idObject: 18554
+      };
+      var alias = new Alias(javaObject);
+      var alias2 = new Alias(javaObject);
+      alias.update(alias2);
+      assert.equal(alias.isComplete(), false);
+    });
   });
 
 });

frontend-js/src/test/js/map/data/MapModel-test.js

@@ -7,6 +7,7 @@ var LayoutData = require('../../../../main/js/map/data/LayoutData');
 var MapModel = require('../../../../main/js/map/data/MapModel');
 var NetworkError = require('../../../../main/js/NetworkError');
 var PointData = require('../../../../main/js/map/data/PointData');
+var ServerConnector = require('../../ServerConnector-mock');
 
 var assert = require('chai').assert;
 

frontend-js/src/test/js/map/surface/ReactionSurface-test.js

@@ -23,7 +23,7 @@ describe('ReactionSurface', function () {
     assert.ok(reactionOverlay.getColor());
     assert.ok(reactionOverlay.getWidth());
     assert.ok(reactionOverlay.getBounds());
-    assert.ok(reactionOverlay.getReactionData());
+    assert.ok(reactionOverlay.getBioEntity());
     assert.ok(reactionOverlay.getCustomMap());
     assert.ok(reactionOverlay.getId());
     assert.ok(typeof reactionOverlay.getColor() === "string");
@@ -44,7 +44,7 @@ describe('ReactionSurface', function () {
       assert.ok(reactionOverlay.getColor());
       assert.ok(reactionOverlay.getWidth());
       assert.ok(reactionOverlay.getBounds());
-      assert.ok(reactionOverlay.getReactionData());
+      assert.ok(reactionOverlay.getBioEntity());
       assert.ok(reactionOverlay.getCustomMap());
       assert.ok(reactionOverlay.getId());
       assert.ok(typeof reactionOverlay.getColor() === "string");