Merge remote-tracking branch 'origin/genomics' into frontend-refactor

Conflicts:
	web/src/main/webapp/index.xhtml
	web/src/main/webapp/resources/js/CustomMap.js

web/src/main/java/lcsb/mapviewer/bean/GalaxyBean.java

@@ -149,7 +149,7 @@ public class GalaxyBean extends AbstractManagedBean implements Serializable {
 		} catch (InvalidColorSchemaException e) {
 			status = "Problem with input file: " + e.getMessage();
 		} catch (Exception e) {
-			logger.error(e);
+			logger.error(e, e);
 			status = "Internal server error. More details can be found in log file.";
 		}
 	}

web/src/main/webapp/index.xhtml

@@ -45,11 +45,73 @@ function initMap(){
 		    customTouchInterface: windowsTouchInterface,
 		    debug:minerva.GuiConnector.getParams['debug']!==undefined,
 		});
+<<<<<<< HEAD
 	}).then(function(result){
 		customMap = result;
 	}).catch(function(rejectReason){
 		minerva.GuiConnector.alert(rejectReason);
 	});
+=======
+		logger.debug(configuration);
+	
+    ServerConnector.setCustomMap(customMap);  
+		GuiConnector.showGoogleMap();
+		
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "search"));
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "missingConnection"));
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "drug",true, true));
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "chemical",#{chemicalMB.linkedToDisease()}, #{chemicalMB.linkedToDisease() == true}));
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "mirna",true, true));
+		ServerConnector.addOverlayCollection(new OverlayCollection(customMap, "comment",false, true));
+		
+		customMap.refreshOverlays();
+
+		
+		if (GuiConnector.getParams["search"]!=undefined) {
+			searchPanel.search(GuiConnector.getParams["search"]);
+		}
+		
+		if (GuiConnector.getParams["comments"]=="on") {
+			document.getElementById('comment_checkbox').click();
+		}
+		if (GuiConnector.getParams["layout"]!=undefined) {
+			for (var i=0;i<configuration.MAPS.length;i++){
+							if (configuration.MAPS[i].name===GuiConnector.getParams["layout"]) {
+											if (configuration.MAPS[i].inputDataAvailable==="true") {
+												customMap.addSelectedLayout(configuration.MAPS[i].idObject, GuiConnector.getParams["layout"])
+											} else {
+												customMap.openLayoutByName(GuiConnector.getParams["layout"])
+											}
+							}
+			}
+		}
+
+  }
+	//when I try to hide legend from the beginning or in the same thread it's hidden forever... ;/
+	setTimeout(function() {
+		GuiConnector.hideLegend();
+		var submodelId = GuiConnector.getParams["submap"];
+		if (submodelId!=undefined) {
+			_createSubmodelDialog([{name:'submodelId', value: submodelId}]);
+			//for some reason the call above is not sync (even though it's required)
+			var waitingForResponse = setInterval(function() {
+				if (GuiConnector.getJsPopupForSubmodelId(submodelId)!=null) {
+					GuiConnector.openDialog(submodelId);
+					clearInterval(waitingForResponse);
+					if (GuiConnector.getParams["zoom"]!=undefined){
+						customMap.setZoom(submodelId,parseInt(GuiConnector.getParams["zoom"]));
+					}
+					if (GuiConnector.getParams["x"]!=undefined && GuiConnector.getParams["y"]!=undefined){
+						var x = GuiConnector.getParams["x"];
+						var y = GuiConnector.getParams["y"];
+						var point = new google.maps.Point(x, y);
+						customMap.setCenter(submodelId,point);
+					}
+				}
+			},100);
+		}
+	}, 0);
+>>>>>>> refs/remotes/origin/genomics
 }
 
 //]]>