Merge branch 'hotfix/changeAsSelectionMapping'

app.json

@@ -7,7 +7,7 @@
     /**
      * The version of the application.
      */
-    "version": "3.0.0",
+    "version": "3.0.1",
 
     /**
      * The relative path to the application's markup file (html, jsp, asp, etc.).

app/Application.js

@@ -9,6 +9,8 @@ Ext.define('metExploreViz.Application', {
     name: 'metExploreViz',
 
     stores: [
+        'metExploreViz.view.form.selectMapping.MappingStore',
+        'mappingStore',
         'metExploreViz.view.form.selectCondition.ConditionStore',
         'conditionStore'
 
@@ -17,7 +19,7 @@ Ext.define('metExploreViz.Application', {
     
     launch: function () {
         Ext.create('metExploreViz.view.form.selectCondition.ConditionStore');
-
+        Ext.create('metExploreViz.view.form.selectMapping.MappingStore');
 
         // TODO - Launch the application
     },

app/view/form/selectCondition/ConditionModel.js

@@ -7,8 +7,10 @@ Ext.define('metExploreViz.view.form.selectCondition.ConditionModel', {
 	extend: 'Ext.data.Model',
 	fields: [
 		{
-			name: 'name', type: 'string',
-			name: 'biologicalType', type: 'string',
+			name: 'name',
+			type: 'string',
+			name: 'biologicalType',
+			type: 'string'
 		}
 	]
 });
\ No newline at end of file

app/view/form/selectConditionForm/SelectConditionFormController.js

@@ -587,6 +587,10 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
 		var captions = view.lookupReference('discreteCaptions');
 		var scaleCaption = view.lookupReference('scaleCaption');
 	    var selectCondition = view.lookupReference('selectCondition');
+
+		var selectConditionType = view.lookupReference('selectConditionType');
+		var dataType = selectConditionType.getValue();
+
 		var selectedCondition = selectCondition.getValue();
 		var networkVizSession = _metExploreViz.getSessionById("viz");
         var colorStore;
@@ -696,8 +700,10 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
 
 												var  mappingName = selectedCondition.split(" / ")[0];
 												var  conditionName = selectedCondition.split(" / ")[1];
-
-												metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, color.getName(), color.getValue());
+												if(dataType==="As selection")
+													metExploreD3.GraphStyleEdition.setCollectionStyleAsSelectionMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, "Identified", color.getValue())
+												else
+													metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, color.getName(), color.getValue());
 
 											}
 											else
@@ -752,8 +758,10 @@ Ext.define('metExploreViz.view.form.selectConditionForm.SelectConditionFormContr
 
 											var mappingName = selectedCondition.split(" / ")[0];
 											var conditionName = selectedCondition.split(" / ")[1];
-
-											metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, color.getName(), color.getValue());
+											if(dataType==="As selection")
+												metExploreD3.GraphStyleEdition.setCollectionStyleAsSelectionMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, "Identified", color.getValue())
+											else
+												metExploreD3.GraphStyleEdition.setCollectionStyleDiscreteMapping(aStyleFormParent.target, aStyleFormParent.attrType, aStyleFormParent.attrName, aStyleFormParent.biologicalType, conditionName, mappingName, color.getName(), color.getValue());
 										});
 								},
 								scope: me

app/view/form/selectMapping/MappingModel.js

+/**
+ * @author MC
+ * (a)description class to control contion selection panel and to draw mapping in the mapping story
+ */
+
+Ext.define('metExploreViz.view.form.selectMapping.MappingModel', {
+	extend: 'Ext.data.Model',
+	fields: [
+		{
+			name: 'name', type: 'string'
+		}
+	]
+});
\ No newline at end of file

app/view/form/selectMapping/MappingStore.js

+/**
+ * @author MC
+ * (a)description class to control contion selection panel and to draw mapping in the mapping story
+ */
+
+Ext.define('metExploreViz.view.form.selectMapping.MappingStore', {
+	extend: 'Ext.data.Store',
+	alias: 'store.MappingStore',
+	requires: [
+		"metExploreViz.view.form.selectMapping.MappingModel"
+	],
+	model: 'metExploreViz.view.form.selectMapping.MappingModel',
+	storeId: 'mappingStore',
+	data: [{name:'None'}],
+	listeners: {
+		add: function(store, records) {
+			// if(store.count()==1)
+
+		}
+	}
+});
\ No newline at end of file

app/view/form/selectMapping/SelectMapping.js

@@ -8,17 +8,17 @@ Ext.define('metExploreViz.view.form.selectMapping.SelectMapping', {
         alias: 'widget.selectMapping',
         requires: [
                 "metExploreViz.view.form.selectMapping.SelectMappingController",
+                "metExploreViz.view.form.selectMapping.MappingStore",
                 "metExploreViz.view.form.selectMapping.SelectMappingModel"
         ],
         controller: "form-selectMapping-selectMapping",
         viewModel: {
             type: "form-selectMapping-selectMapping"
         },
-        store: {
-            fields: ['name'],
-            data: [{name:'None'}]
-        },
         listeners: {
+            beforerender: function(c) {
+                this.setStore(Ext.getStore("mappingStore"));
+            },
             render: function(c) {
                 new Ext.ToolTip({
                     target: c.getEl(),

app/view/form/selectMappingForExtraction/SelectMappingForExtraction.js

+/**
+ * @author MC
+ * (a)description combobox to select condition in mapping
+ * selectMappingForExtraction
+ */
+Ext.define('metExploreViz.view.form.selectMappingForExtraction.SelectMappingForExtraction', {
+    extend: 'Ext.window.Window',
+	alias: 'widget.selectMappingForExtraction',
+	requires: [
+	    "metExploreViz.view.form.selectMappingForExtraction.SelectMappingForExtractionController"
+    ],
+    controller: "form-selectMappingForExtraction-selectMappingForExtraction",
+
+    title: 'Continuous color scale mapping editor',
+    height: "400px",
+    maxWidth: 600,
+    minWidth: 600,
+    x: 100,
+    y: 100,
+    maxHeight: 365,
+    minHeight: 365,
+    layout:{
+        type:'vbox',
+        align:'stretch'
+    },
+    items: [
+        {
+            margin: "10 10 10 10",
+            xtype: "selectMapping",
+            multiSelect: true,
+            reference: "selectMappingForExtraction"
+        },
+        {
+            xtype: "panel",
+            reference: "buttonPanel",
+            layout:{
+                type:'hbox',
+                pack : 'end'
+            },
+            items:[
+                {
+                    margin: "5 5 5 5",
+                    xtype: 'button',
+                    reference: 'okButton',
+                    text : 'OK'
+                },
+                {
+                    margin: "5 15 5 5",
+                    xtype: 'button',
+                    reference: 'cancelButton',
+                    text : 'Cancel'
+                }
+            ]
+        }
+    ]
+});
\ No newline at end of file

app/view/form/selectMappingForExtraction/SelectMappingForExtractionController.js

+/**
+ * @author MC
+ * (a)description class to control contion selection panel and to draw mapping in the mapping story
+ */
+
+Ext.define('metExploreViz.view.form.selectMappingForExtraction.SelectMappingForExtractionController', {
+	extend: 'Ext.app.ViewController',
+	alias: 'controller.form-selectMappingForExtraction-selectMappingForExtraction',
+
+/**
+ * Aplies event linsteners to the view
+ */
+	init:function(){
+		var me 		= this,
+		viewModel   = me.getViewModel(),
+		view      	= me.getView();
+
+		view.on({
+			show : function(that){
+				var store = Ext.getStore("mappingStore");
+				store.filter(function (mapping) {
+					console.log(mapping.get("name"));
+					return mapping.get("name")!=="None";
+				})
+			},
+			close :  function(that){
+				var store = Ext.getStore("mappingStore");
+				store.clearFilter();
+			}
+		});
+
+		view.lookupReference('okButton').on({
+			click : function(that){
+				if(view.lookupReference('selectMappingForExtraction').getValue() && view.lookupReference('selectMappingForExtraction').getValue()!=="None"){
+					var selectedMappings = view.lookupReference('selectMappingForExtraction').getValue();
+					var nodesToLinks = _metExploreViz.getSessionById("viz").getD3Data().getNodes()
+						.filter(function(node){ return node.mappingDatas.length!==0;})
+						.filter(function (node) {
+							return node.getMappingDatas()
+								.filter(map => selectedMappings.includes(map.getMappingName())).length !==0;
+						})
+						.map(node => node.getId());
+					console.log(nodesToLinks);
+
+					metExploreD3.GraphFunction.keepOnlySubnetwork(nodesToLinks);
+				}
+				view.close();
+			}
+		});
+
+		view.lookupReference('cancelButton').on({
+			click : function(that){
+				view.close();
+			}
+		});
+	}
+});
\ No newline at end of file

app/view/main/Main.js

@@ -16,6 +16,7 @@ Ext.define('metExploreViz.view.main.Main', {
         'metExploreViz.view.main.MainController',
         'metExploreViz.view.main.MainModel',
         'metExploreViz.view.panel.networkPanel.NetworkPanel',
+        "metExploreViz.view.form.selectMapping.MappingStore",
         "metExploreViz.view.form.selectCondition.ConditionStore"
     ],
 

app/view/main/MainController.js

@@ -9,6 +9,8 @@ Ext.define('metExploreViz.view.main.MainController', {
 
     alias: 'controller.main',
     stores: [
+        'metExploreViz.view.form.selectMapping.MappingStore',
+        'mappingStore',
         'metExploreViz.view.form.selectCondition.ConditionStore',
         'conditionStore'
 

app/view/menu/viz_ExtractSubNetworkMenu/Viz_ExtractSubNetworkMenuController.js

 Ext.define('metExploreViz.view.menu.viz_ExtractSubNetworkMenu.Viz_ExtractSubNetworkMenuController', {
 	extend: 'Ext.app.ViewController',
 	alias: 'controller.menu-vizExtractSubNetworkMenu-vizExtractSubNetworkMenu',
-
+	requires: [
+		"metExploreViz.view.form.selectMappingForExtraction.SelectMappingForExtraction"
+	],
 /**
  * Aplies event linsteners to the view
  */
@@ -9,12 +11,14 @@ Ext.define('metExploreViz.view.menu.viz_ExtractSubNetworkMenu.Viz_ExtractSubNetw
 		var me 		= this,
 		viewModel   = me.getViewModel(),
 		view      	= me.getView();
-
+	var win =
 		view.lookupReference('keepOnlySubnetworkFromMapping').on({
 			click : function(){
-                var session = _metExploreViz.getSessionById('viz');
-                console.log(session.getNodesMap());
-                metExploreD3.GraphFunction.keepOnlySubnetwork(session.getNodesMap());
+
+				var win = Ext.create("metExploreViz.view.form.selectMappingForExtraction.SelectMappingForExtraction");
+
+				win.show();
+
 			},
 			scope : me
 		});

app/view/menu/viz_MiningMenu/Viz_MiningMenu.js

@@ -32,7 +32,6 @@ Ext.define('metExploreViz.view.menu.viz_MiningMenu.Viz_MiningMenu', {
                 text: 'Highlight Subnetwork',
                 reference :'highlightSubnetwork',
                 id :'highlightSubnetwork',
-                tooltip:'Highlight sub-network based on node selection or mapped nodes',
                 iconCls:'highlightSubnetwork',
                 hidden:true
             },
@@ -40,14 +39,12 @@ Ext.define('metExploreViz.view.menu.viz_MiningMenu.Viz_MiningMenu', {
                 text: 'Highlight sink',
                 reference :'highlightSink',
                 id :'highlightSink',
-                tooltip:'Highlight Sink',
                 iconCls:'highlightSink'
             },
             {
                 text: 'Highlight source',
                 reference :'highlightSource',
                 id :'highlightSource',
-                tooltip:'Highlight Source',
                 iconCls:'highlightSource'
             },{
                 text: 'Extract Subnetwork',
@@ -56,8 +53,7 @@ Ext.define('metExploreViz.view.menu.viz_MiningMenu.Viz_MiningMenu', {
                 id:'vizExtractSubNetworkID',
                 reference:'vizExtractSubNetworkID',
                 padding:'0 0 0 0',
-                iconCls:'subnetwork',
-                tooltip:'Extract sub-network based on node selection or node mapping'
+                iconCls:'subnetwork'
             }
             //  {
             //     text: 'Extract Subnetwork',action:'subnetwork',tooltip:'Extract sub-network based on node selection',iconCls:'subnetwork',

app/view/panel/networkPanel/NetworkPanelController.js

@@ -7,6 +7,7 @@ Ext.define('metExploreViz.view.panel.networkPanel.NetworkPanelController', {
 	extend: 'Ext.app.ViewController',
 	alias: 'controller.panel-networkPanel-networkPanel',
 	stores: [
+		'metExploreViz.view.form.selectMapping.MappingStore',
 		'metExploreViz.view.form.selectCondition.ConditionStore'
 
 		// TODO: add global / shared stores here
@@ -21,6 +22,7 @@ Ext.define('metExploreViz.view.panel.networkPanel.NetworkPanelController', {
 		view      	= me.getView();
 
 		Ext.create('metExploreViz.view.form.selectCondition.ConditionStore');
+		Ext.create('metExploreViz.view.form.selectMapping.MappingStore');
 
 		view.on({
 			afterrender : me.initParams,