Merge branch '176-drugs-show-all-content-and-alignment' into 'master'

Resolve "Drugs - Show all - content and alignment"

Closes #176

See merge request !89

frontend-js/src/main/js/gui/topMenu/TopMenu.js

@@ -117,7 +117,7 @@ TopMenu.prototype._createGui = function() {
 
   var refreshCommentButton = Functions.createElement({
     type : "button",
-    className : "overview_button",
+    className : "minerva-overview-button",
     name : "refreshCommentButton",
     content : "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>",
     style : "display:none",
@@ -127,7 +127,7 @@ TopMenu.prototype._createGui = function() {
 
   var clearButton = Functions.createElement({
     type : "button",
-    className : "overview_button",
+    className : "minerva-overview-button",
     name : "clearButton",
     content : "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i>CLEAR",
   });

frontend-js/src/main/js/map/Submap.js

 "use strict";
 
+/* exported logger */
+
 var logger = require('../logger');
 var AbstractCustomMap = require('./AbstractCustomMap');
 var CustomMapOptions = require('./CustomMapOptions');

frontend-js/src/main/js/map/window/AbstractInfoWindow.js

@@ -32,19 +32,17 @@ function AbstractInfoWindow(params) {
   var onOverlayFullViewChanged = function(e) {
     var self = e.object;
     // first change the content of the element
-    return self.update().then(
-        function() {
-          if (e.newVal) {
-            var element = new IdentifiedElement({
-              objectId : self.getElementId(),
-              modelId : self.getCustomMap().getId(),
-              type : self.getElementType()
-            });
-
-            return self.getCustomMap().getTopMap().retrieveOverlayDetailDataForElement(element,
-                self.getOverlayFullViewArray());
-          }
+    return self.update().then(function() {
+      if (e.newVal) {
+        var element = new IdentifiedElement({
+          objectId : self.getElementId(),
+          modelId : self.getCustomMap().getId(),
+          type : self.getElementType()
         });
+        var topMap = self.getCustomMap().getTopMap();
+        return topMap.retrieveOverlayDetailDataForElement(element, self.getOverlayFullViewArray());
+      }
+    });
 
   };
 
@@ -222,7 +220,11 @@ AbstractInfoWindow.prototype.createOverlayInfoDiv = function(overlay, data) {
  * @returns {String} with a div for drug overlay information
  */
 AbstractInfoWindow.prototype._createDrugInfoDiv = function(overlay, data) {
-  return this._createTargetInfoDiv(overlay, data, "Interacting drugs");
+  return this._createTargetInfoDiv({
+    overlay : overlay,
+    data : data,
+    name : "Interacting drugs"
+  });
 };
 
 /**
@@ -408,7 +410,11 @@ AbstractInfoWindow.prototype.update = function() {
   return this._updateContent();
 };
 
-AbstractInfoWindow.prototype._createTargetInfoDiv = function(overlay, data, name) {
+AbstractInfoWindow.prototype._createTargetInfoDiv = function(params) {
+  var overlay = params.overlay;
+  var data = params.data;
+  var name = params.name;
+
   var self = this;
   var result = document.createElement("div");
 
@@ -472,6 +478,11 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
   table.appendChild(header);
   var row;
 
+  var onclick = function() {
+    // ';' enforces single query (in case there are ',' characters in the name)
+    return overlay.searchByQuery(this.innerHTML + ";");
+  };
+
   var count = 0;
   for ( var searchId in data) {
     if (data.hasOwnProperty(searchId)) {
@@ -491,10 +502,18 @@ AbstractInfoWindow.prototype._createTableForTargetDiv = function(data, overlay)
           }
         }
       }
-      row.appendChild(Functions.createElement({
+      var link = Functions.createElement({
+        type : "a",
+        onclick : onclick,
+        href : "#",
+        content : nameContent,
+      });
+
+      var nameTd = Functions.createElement({
         type : "td",
-        content : nameContent
-      }));
+      });
+      nameTd.appendChild(link);
+      row.appendChild(nameTd);
 
       var referencesCell = Functions.createElement({
         type : "td",
@@ -550,7 +569,11 @@ AbstractInfoWindow.prototype.getGuiUtils = function() {
  * @returns DOM element with a div for comment overlay information
  */
 AbstractInfoWindow.prototype._createChemicalInfoDiv = function(overlay, data) {
-  return this._createTargetInfoDiv(overlay, data, "Interacting chemicals");
+  return this._createTargetInfoDiv({
+    overlay : overlay,
+    data : data,
+    name : "Interacting chemicals",
+  });
 };
 
 /**
@@ -561,7 +584,11 @@ AbstractInfoWindow.prototype._createChemicalInfoDiv = function(overlay, data) {
  * @returns DOM element with a div for comment overlay information
  */
 AbstractInfoWindow.prototype._createMiRnaInfoDiv = function(overlay, data) {
-  return this._createTargetInfoDiv(overlay, data, "Interacting Micro RNAs");
+  return this._createTargetInfoDiv({
+    overlay : overlay,
+    data : data,
+    name : "Interacting Micro RNAs"
+  });
 };
 
 /**

frontend-js/src/test/js/Export-test.js

 "use strict";
 
 /* exported logger */
+/* exported assert */
 
 var Export = require('../../main/js/Export');
 var logger = require('./logger');

frontend-js/src/test/js/map/window/AliasInfoWindow-test.js

@@ -125,6 +125,32 @@ describe('AliasInfoWindow', function() {
     });
   });
 
+  it("createChemicalOverlayInfoDiv", function() {
+    var map, ie, aliasWindow, oc;
+    return ServerConnector.getProject().then(function(project) {
+      map = helper.createCustomMap(project);
+
+      oc = helper.createChemicalDbOverlay(map);
+
+      ie = new IdentifiedElement({
+        id : 329170,
+        modelId : map.getId(),
+        type : "ALIAS"
+      });
+
+      return map.getModel().getByIdentifiedElement(ie, true);
+    }).then(function(alias) {
+      aliasWindow = new AliasInfoWindow({
+        alias : alias,
+        map : map
+      });
+      return oc.getDetailDataByIdentifiedElement(ie, true);
+    }).then(function(data) {
+      var overlayDiv = aliasWindow.createOverlayInfoDiv(oc, data);
+      assert.ok(functions.isDomElement(overlayDiv));
+    });
+  });
+
   it("createCommentOverlayInfoDiv", function() {
     var map = helper.createCustomMap();
 

frontend-js/testFiles/apiCalls/projects/sample/models/all/bioEntities/elements/id=329170&token=MOCK_TOKEN_ID&

+[{"elementId":"sa32","symbol":null,"formerSymbols":[],"other":{"structuralState":null,"modifications":[]},"notes":"","references":[{"resource":"622","link":"http://www.ncbi.nlm.nih.gov/gene/622","id":860352,"type":"ENTREZ"}],"modelId":15781,"synonyms":[],"fullName":null,"complexId":null,"type":"Protein","abbreviation":null,"compartmentId":null,"name":"BDH1","bounds":{"x":1225.7682370820667,"width":80.0,"y":66.0,"height":40.0},"formula":null,"id":329170,"linkedSubmodel":null,"hierarchyVisibilityLevel":"0"}]
\ No newline at end of file

rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.api;
 
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Comparator;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -200,6 +201,23 @@ public abstract class BaseRestImpl {
 		for (Target target : targets) {
 			result.add(prepareTarget(target, models));
 		}
+		result.sort(new Comparator<Map<String, Object>>() {
+
+			@Override
+			public int compare(Map<String, Object> o1, Map<String, Object> o2) {
+				List<?> targetedObjects1 = (List<?>) o1.get("targetElements");
+				List<?> targetedObjects2 = (List<?>) o2.get("targetElements");
+				Integer size1 = 0;
+				Integer size2 = 0;
+				if (targetedObjects1 != null) {
+					size1 = targetedObjects1.size();
+				}
+				if (targetedObjects2 != null) {
+					size2 = targetedObjects2.size();
+				}
+				return -size1.compareTo(size2);
+			}
+		});
 		return result;
 	}
 
@@ -238,5 +256,4 @@ public abstract class BaseRestImpl {
 		}
 	}
 
-
 }