It fixes issue ispyb#499

js/core/app/exi.js

@@ -67,6 +67,7 @@ function Exi(args) {
 
 	this.credentialManager.onActiveProposalChanged.attach(function(sender){
 		_this.mainMenu.populateCredentialsMenu();
+
 	});
 
 

js/core/app/proposalmanager.js

@@ -242,6 +242,13 @@ ProposalManager.prototype.getCrystals = function() {
 	return this.get()[0].crystals;
 };
 
+/**
+* @method getLigands
+*/
+ProposalManager.prototype.getLigands = function() {
+	return this.get()[0].ligands;
+};
+
 /**
 * @method getProteinByAcronym
 */

js/core/controller/proposalexicontroller.js

@@ -63,5 +63,24 @@ ProposalExiController.prototype.init = function() {
 			EXI.addMainPanel(mainView);
 			mainView.load(this.params['containerId']);
 		}).enter(this.setPageBackground);
+
+
+		Path.map("#/ligands/list").to(function() {
+
+			EXI.clearNavigationPanel();
+			EXI.hideNavigationPanel();
+
+			EXI.setLoadingMainPanel("Searching for ligands");
+			var main = new LigandsMainView();
+			EXI.addMainPanel(main);			
+			var onSuccessProtein = function(sender, ligands) {								
+				main.load(ligands);
+				EXI.setLoadingMainPanel(false);
+			};
+			EXI.getDataAdapter({onSuccess : onSuccessProtein}).proposal.proposal.getLigandsByProposalId();
+		}).enter(this.setPageBackground);
+
+
+
 
 };

js/core/view/shipping/containerspreadsheet.js

@@ -251,7 +251,8 @@ ContainerSpreadSheet.prototype.getSamplesData = function(puck) {
 						diffraction.axisRange,
 						diffraction.minOscWidth,
 						getValue(diffraction["observedResolution"]),  
-						sample.comments
+						sample.comments,
+						sample.structureStage
                     ]
                 );
         }
@@ -340,7 +341,14 @@ ContainerSpreadSheet.prototype.getHeader = function() {
 			{ text :'Tot Rot. <br />Angle', id :'axisRange',column : {width : 60}},
 			{ text :'Min Osc.<br />Angle', id :'minOscWidth',column : {width : 60}},		
             { text :'Observed <br />resolution', id : 'Pre-observed resolution', column : {width : 80}}, 
-            { text :'Comments', id :'Comments', column : {width : 200}}
+			{ text :'Comments', id :'Comments', column : {width : 200}},
+			{ text :'Ligands', id : 'Ligands', column : {
+				width : 100,  
+				type: 'autocomplete',
+				filter: 'true',
+				source: this.getLigandsGroupName()
+			}
+			}
             ];
 
 
@@ -390,6 +398,9 @@ ContainerSpreadSheet.prototype.getPuck = function() {
 		sample["smiles"] = rows[i]["Smiles"];
 		sample["location"]= rows[i]["location"];
 		sample["comments"] = rows[i]["Comments"];
+
+		sample["structureStage"] = rows[i]["Ligands"];
+
         var proteins = [];
 		if (sample["crystalVO"] == null){
 			sample["crystalVO"] = {};
@@ -448,6 +459,10 @@ ContainerSpreadSheet.prototype.getProteinsByAcronym = function(acronym) {
 	return this.proteins[acronym];
 };
 
+ContainerSpreadSheet.prototype.getLigandsGroupName = function() {
+	return _.concat([""], _.uniq(_.map(EXI.proposalManager.getLigands(), function(o) {return o.groupName})));
+};
+
 /**
 * Returns an object containing the crystal information given the value at the crystal form column
 *

js/core/view/shipping/editcrystalformview.js

@@ -62,6 +62,7 @@ EditCrystalFormView.prototype.render = function () {
     var html = "";
 	var crystalName = "";
 
+
     dust.render("crystal.edit.form.template", this.crystal, function(err, out){
 		html = out;
 	});

js/core/view/shipping/editcrystalstructure.js

@@ -4,6 +4,9 @@ function EditCrystalStructure(args) {
 	this.width = 600;
 	this.height = 500;
 	this.showTitle = true;
+
+	this.types =  ["PDB", "FASTA"];
+	this.label = "Group Name";
 	if (args != null) {
 		if (args.showTitle != null) {
 			this.showTitle = args.showTitle;
@@ -14,6 +17,12 @@ function EditCrystalStructure(args) {
 		if (args.height != null) {
 			this.height = args.height;
 		}
+		if (args.types != null) {
+			this.types = args.types;
+		}
+		if (args.label != null) {
+			this.label = args.label;
+		}
 	}
 
 	this.onSaved = new Event(this);
@@ -33,12 +42,22 @@ EditCrystalStructure.prototype.getPanel = function () {
 	return this.panel;
 };
 
+/**
+ * Crystal might be null and then it is store as proposal
+ */
 EditCrystalStructure.prototype.load = function (crystal) {
-	var _this = this;
 
-	this.crystal = crystal;
-
-	this.crystal.url = EXI.getDataAdapter().mx.crystal.getSaveStructureURL(this.crystal.crystalId);
+	if (crystal){
+		this.crystal = crystal;	
+
+		this.crystal.url = EXI.getDataAdapter().mx.crystal.getSaveStructureURL(this.crystal.crystalId);
+	}
+	else{
+		this.crystal = {};
+		this.crystal.url = EXI.getDataAdapter().proposal.proposal.saveStructure();
+	}
+	this.crystal.label = this.label;
+	this.crystal.types = this.types;
 	dust.render("structure.crystal.edit.form.template", this.crystal, function (err, out) {
 		html = out;
 	}); 
@@ -55,13 +74,19 @@ EditCrystalStructure.prototype.save = function () {
 		e.preventDefault();
 		/** Setting the filename */
 		$("#structure-fileName").val($("#structure-input-file").val().split('\\').pop());
-		var formData = new FormData(this);		
+		var formData = new FormData(this);	
+		_this.panel.setLoading();
+
 		$.ajax({
 			url: this.action,
 			type: 'POST',
 			data: formData,
 			success: function (data) {
-				_this.onSaved.notify();
+				_this.onSaved.notify(data);
+				_this.panel.setLoading(false);
+			},
+			error : function(error){
+				alert("There was an error in the server");
 			},
 			cache: false,
 			contentType: false,

js/core/view/shipping/editligands.js

@@ -0,0 +1,76 @@
+function EditLigands(args) {
+	this.id = BUI.id();
+
+	this.width = 600;
+	this.height = 500;
+	this.showTitle = true;
+	if (args != null) {
+		if (args.showTitle != null) {
+			this.showTitle = args.showTitle;
+		}
+		if (args.width != null) {
+			this.width = args.width;
+		}
+		if (args.height != null) {
+			this.height = args.height;
+		}
+	}
+
+	this.onSaved = new Event(this);
+};
+
+EditLigands.prototype.getPanel = function () {
+
+	this.panel = Ext.create("Ext.panel.Panel", {
+		items: [{
+			html: '<div id="' + this.id + '"></div>',
+			autoScroll: false,
+			padding: this.padding,
+			width: this.width,
+		}]
+	});
+
+	return this.panel;
+};
+
+EditLigands.prototype.load = function (crystal) {
+	var _this = this;
+
+	this.crystal = crystal;
+
+	this.crystal.url = EXI.getDataAdapter().mx.crystal.getSaveStructureURL(this.crystal.crystalId);
+	dust.render("structure.crystal.edit.form.template", this.crystal, function (err, out) {
+		html = out;
+	}); 
+
+	$('#' + this.id).hide().html(html).fadeIn('fast');
+	this.panel.doLayout();
+} 
+
+
+
+EditLigands.prototype.save = function () {
+	var _this = this;	
+	$("#structure-form").submit(function (e) {		
+		e.preventDefault();
+		/** Setting the filename */
+		$("#structure-fileName").val($("#structure-input-file").val().split('\\').pop());
+		var formData = new FormData(this);		
+		$.ajax({
+			url: this.action,
+			type: 'POST',
+			data: formData,
+			success: function (data) {
+				_this.onSaved.notify();
+			},
+			cache: false,
+			contentType: false,
+			processData: false
+		});
+	});
+
+	$("#structure-form").submit();
+
+};
+
+

js/ispyb-client/proposal/proposaldataadapter.js

@@ -28,6 +28,14 @@ ProposalDataAdapter.prototype.synchSMIS= function(){
 	this.get('/{token}/proposal/{proposal}/update'.format([]));
 };
 
+ProposalDataAdapter.prototype.getLigandsByProposalId= function(){
+	this.get('/{token}/proposal/{proposal}/ligands/list');
+};
+
+ProposalDataAdapter.prototype.saveStructure= function(){
+	return this.getUrl('/{token}/proposal/{proposal}/structure/save');
+};
+
 ProposalDataAdapter.prototype.update= function(){
 	if (EXI != null){
 		if (EXI.proposalManager != null){

js/mx/controller/proteincontroller.js

@@ -54,6 +54,11 @@ ProteinController.prototype.init = function() {
 			};
 			EXI.getDataAdapter({onSuccess : onSuccessProtein}).mx.protein.getProteinStatsByProposalId();
 	}).enter(this.setPageBackground);
+
+
+
+
+
 	Path.rescue(this.notFound);
 
 };

js/mx/menu/mxmainmenu.js

@@ -15,7 +15,10 @@ MXMainMenu.prototype.getHelpMenu = MainMenu.prototype.getHelpMenu;
 MXMainMenu.prototype.getShipmentItem = MainMenu.prototype.getShipmentItem;
 MXMainMenu.prototype.getDataExplorerMenu = MainMenu.prototype.getDataExplorerMenu;
 
+
+
 MXMainMenu.prototype.getMenuItems = function() {
+
 	return [
 		this.getHomeItem(),
 		this.getShipmentItem(),
@@ -26,7 +29,7 @@ MXMainMenu.prototype.getMenuItems = function() {
                 disabled : false,
                 handler : function(){
                     location.hash = "#/protein/list";
-                }
+				}
 	    	},
 	    	{
                 text : this._convertToHTMLWhiteSpan("Prepare Experiment"),

js/mx/menu/mxmanagermenu.js

@@ -25,20 +25,19 @@ MXManagerMenu.prototype.getMenuItems = function() {
     	this.getShipmentItem(),
     	{
                 text : this._convertToHTMLWhiteSpan("Prepare Experiment"),
-                cls : 'ExiSAXSMenuToolBar',
-                disabled : false,
+				cls : 'ExiSAXSMenuToolBar',				               
                 handler : function(){
                     location.hash = "/mx/prepare/main";
 
-				}
+				} 
 		},
 		{
-                text : this._convertToHTMLWhiteSpan("Proteins and Crystals <sub style='font-size:10px;color:orange'>NEW</sub>"),
+                text : this._convertToHTMLWhiteSpan("Samples <sub style='font-size:10px;color:orange'>NEW</sub>"),
                 cls : 'ExiSAXSMenuToolBar',
-                disabled : false,
-                handler : function(){
+				menu : this.getProteinCrystalsMenu() 
+                /*handler : function(){
                     location.hash = "#/protein/list";
-                }
+                }*/
 	    },
 		{
 				text : this._convertToHTMLWhiteSpan("Data Explorer"),
@@ -91,6 +90,45 @@ MXManagerMenu.prototype.getMenuItems = function() {
 	];
 };
 
+
+
+MXManagerMenu.prototype.getProteinCrystalsMenu = function() {
+	var _this = this;
+	function onItemCheck(item, checked) {
+		if (item.text == "Autoproc Scaling Statistics") {
+			var scatteringForm = new ScatteringForm();
+
+			var keys = ["ISA", "rPimWithinIPlusIMinus","anomalousMultiplicity","multiplicity","resolutionLimitLow","ccHalf",
+			"strategySubWedgeOrigId","completeness","rMerge","anomalous","meanIOverSigI","ccAno","autoProcScalingId",
+			"nTotalObservations","sigAno","rMeasWithinIPlusIMinus","anomalousCompleteness","resolutionLimitHigh",
+			"fractionalPartialBias","rMeasAllIPlusIMinus","nTotalUniqueObservations","rPimAllIPlusIMinus"];
+
+			var scatteringData = {title : "AutoprocIntegrator", keys : keys};
+
+			scatteringForm.load(scatteringData);
+			scatteringForm.show();
+		}
+	}
+
+	return Ext.create('Ext.menu.Menu', {
+		items : [
+					{
+						text 	: 'Proteins & Crystals',						
+						handler : function(){
+                    		location.hash = "#/protein/list";
+                		}
+					},
+					{
+						text : 'Ligands',
+						icon : '../images/icon/macromolecule.png',
+						handler : function(){
+                    		location.hash = "#/ligands/list";
+                		}
+					}
+			] 
+	});
+};
+
 MXManagerMenu.prototype.getManagerMenu = function() {
 	var _this = this;
 	function onItemCheck(item, checked) {
@@ -118,7 +156,7 @@ MXManagerMenu.prototype.getManagerMenu = function() {
 								items: [
 									{
 										text: 'Autoproc Scaling Statistics',
-										icon : '../images/icon/ic_insert_chart_black_36dp.png',
+										//icon : '../images/icon/ic_insert_chart_black_36dp.png',
 										handler: onItemCheck,
 										disabled : false
 									}