Merge branch 'dev-2.1'

src/index.html

@@ -11,7 +11,7 @@
 
 
   <!-- Pull in correct theme configuration, then use Require.js to manage dependencies -->
-  <script id="loader" type="text/javascript" src="/metacatui/loader.js?v=2.1.0" 
+  <script id="loader" type="text/javascript" src="/metacatui/loader.js?v=2.1.1" 
   	data-theme="default"
   	data-metacat-context="metacat"
   	data-map-key="YOUR-GOOGLE-MAPS-API-KEY"

src/js/app.js

@@ -250,6 +250,12 @@ function(Bootstrap, AppView, AppModel) {
 				return;
 			}
 
+			//Don't route to URLs with the DataONE API, which are sometimes proxied
+			// via Apache ProxyPass so start with the MetacatUI origin
+			if( href.attr.indexOf("/cn/v2/") > 0 || href.attr.indexOf("/mn/v2/") > 0 ){
+				return;
+			}
+
 			var root = location.protocol + "//" + location.host + Backbone.history.options.root;
 			// Remove the MetacatUI (plus a trailing /) from the value in the 'href'
 			// attribute of the clicked element so Backbone.history.navigate works.

src/js/models/NodeModel.js

@@ -141,9 +141,22 @@ define(['jquery', 'underscore', 'backbone'],
 						node.memberSince = node.CN_date_operational;
 
 					node.shortIdentifier = node.identifier.substring(node.identifier.lastIndexOf(":") + 1);
+
 
-					if(node.type == "mn") memberList.push(node);
-					if(node.type == "cn") coordList.push(node);
+					// Push only if the node is not present in the list
+					if ( node.type == "mn" ) {
+						if ( !thisModel.containsObject(node, memberList) ) {
+							memberList.push(node);
+						}
+					} 
+
+					// Push only if the node is not present in the list
+					if ( node.type == "cn" ) {
+						if ( !thisModel.containsObject(node, coordList) ) {
+							coordList.push(node);
+						}
+					} 
+
 				});
 
 				//Save the cn and mn lists in the model when all members have been added
@@ -174,6 +187,13 @@ define(['jquery', 'underscore', 'backbone'],
 				}
 			});
 		},
+
+		// Checks if the node already exists in the List
+		containsObject: function (obj, list) {
+			var res = _.find(list, function(val){ return _.isEqual(obj, val)});
+			return (_.isObject(res))? true:false;
+		},
+
 
 		/*
 		 * Returns true if the given nodeId is a Coordinating Node

src/js/routers/router.js

@@ -46,16 +46,16 @@ function ($, _, Backbone) {
 			// to make this route more inclusive.
 			this.route(/^view\/(.*)$/, "renderMetadata");
 
-			this.on("route", this.trackHash);
-			
+			this.on("route", this.trackPathName);
+
 			// Clear stale JSONLD and meta tags
 			this.on("route", this.clearJSONLD);
 			this.on("route", this.clearHighwirePressMetaTags);
 		},
 
 		//Keep track of navigation movements
 		routeHistory: new Array(),
-		hashHistory: new Array(),
+		pathHistory: new Array(),
 
 		// Will return the last route, which is actually the second to last item in the route history,
 		// since the last item is the route being currently viewed
@@ -66,21 +66,22 @@ function ($, _, Backbone) {
 				return this.routeHistory[this.routeHistory.length-2];
 		},
 
-		trackHash: function(e){
-			if(_.last(this.hashHistory) != window.location.hash)
-				this.hashHistory.push(window.location.hash);
+		trackPathName: function(e){
+			if(_.last(this.pathHistory) != window.location.pathname)
+				this.pathHistory.push(window.location.pathname);
 		},
 
-		//If the user or app cancelled the last route, call this function to revert the window location hash back to the correct value
+		//If the user or app cancelled the last route, call this function to revert
+		// the window location pathname back to the correct value
 		undoLastRoute: function(){
 			this.routeHistory.pop();
 
-			// Remove the last route and hash from the history
-			if(_.last(this.hashHistory) == window.location.hash)
-				this.hashHistory.pop();
+			// Remove the last route and pathname from the history
+			if(_.last(this.pathHistory) == window.location.pathname)
+				this.pathHistory.pop();
 
-			//Change the hash in the window location back
-			this.navigate(_.last(this.hashHistory), {replace: true});
+			//Change the pathname in the window location back
+			this.navigate(_.last(this.pathHistory), {replace: true});
 		},
 
 		renderIndex: function (param) {
@@ -442,7 +443,7 @@ function ($, _, Backbone) {
 		renderLdapSignInSuccess: function(){
 
 			//If there is an LDAP sign in error message
-			if(window.location.hash.indexOf("error=Unable%20to%20authenticate%20LDAP%20user") > -1){
+			if(window.location.pathname.indexOf("error=Unable%20to%20authenticate%20LDAP%20user") > -1){
 				this.renderLdapOnlySignInError();
 			}
 			else{

src/js/themes/arctic/routers/router.js

@@ -37,17 +37,17 @@ function ($, _, Backbone) {
 			// to make this route more inclusive.
 			this.route(/^view\/(.*)$/, "renderMetadata");
 
-			//Track the history of hashes
-			this.on("route", this.trackHash);
-			
+			//Track the history of pathnames
+			this.on("route", this.trackPathName);
+
 			// Clear stale JSONLD and meta tags
 			this.on("route", this.clearJSONLD);
 			this.on("route", this.clearHighwirePressMetaTags);
 		},
 
 		//Keep track of navigation movements
 		routeHistory: new Array(),
-		hashHistory: new Array(),
+		pathHistory: new Array(),
 
 		// Will return the last route, which is actually the second to last item in the route history,
 		// since the last item is the route being currently viewed
@@ -58,21 +58,21 @@ function ($, _, Backbone) {
 				return this.routeHistory[this.routeHistory.length-2];
 		},
 
-		trackHash: function(e){
-			if(_.last(this.hashHistory) != window.location.hash)
-				this.hashHistory.push(window.location.hash);
+		trackPathName: function(e){
+			if(_.last(this.pathHistory) != window.location.pathname)
+				this.pathHistory.push(window.location.pathname);
 		},
 
-		//If the user or app cancelled the last route, call this function to revert the window location hash back to the correct value
+		//If the user or app cancelled the last route, call this function to revert the window location pathname back to the correct value
 		undoLastRoute: function(){
 			this.routeHistory.pop();
 
-			// Remove the last route and hash from the history
-			if(_.last(this.hashHistory) == window.location.hash)
-				this.hashHistory.pop();
+			// Remove the last route and pathname from the history
+			if(_.last(this.pathHistory) == window.location.pathname)
+				this.pathHistory.pop();
 
-			//Change the hash in the window location back
-			this.navigate(_.last(this.hashHistory), {replace: true});
+			//Change the pathname in the window location back
+			this.navigate(_.last(this.pathHistory), {replace: true});
 		},
 
 		renderAPI: function (anchorId) {

src/js/themes/dataone/css/metacatui.css

@@ -1721,9 +1721,9 @@ svg .packages,
 .profile .bar-label.packages{
 	fill: inherit;
 }
-.profile .download-chart .bar-chart .bar.packages,
-.profile .download-chart .bar-chart text.packages{
+.profile .download-chart .bar-chart .bar.packages{
 	fill: #32887F;
+  stroke: #32887F;
 }
   /* Donut charts */
   #metadata-chart,

src/js/themes/dataone/models/AppModel.js

@@ -150,7 +150,7 @@ define(['jquery', 'underscore', 'backbone'],
 				this.set('orcidSearchUrl', this.get('orcidBaseUrl') + '/v1.1/search/orcid-bio?q=');
 
 			//The package service for v2 DataONE API
-			this.set('packageServiceUrl', this.get('baseUrl') + this.get('context') + this.get('d1Service') + '/packages/application%2Fbagit-097/');
+			this.set('packageServiceUrl', this.get('baseUrl') + this.get('d1Service') + '/packages/application%2Fbagit-097/');
 
 			//Only use these settings in production
 			if(this.get("baseUrl").indexOf("search.dataone.org") > -1)

src/js/themes/dataone/routers/router.js

@@ -30,24 +30,24 @@ function ($, _, Backbone) {
 
 		initialize: function(){
 			this.listenTo(Backbone.history, "routeNotFound", this.navigateToDefault);
-			
+
 			// This route handler replaces the route handler we had in the
 			// routes table before which was "view/*pid". The * only finds URL
 			// parts until the ? but DataONE PIDs can have ? in them so we need
 			// to make this route more inclusive.
 			this.route(/^view\/(.*)$/, "renderMetadata");
-			
-			//Track the history of hashes
-			this.on("route", this.trackHash);
-			
+
+			//Track the history of pathnames
+			this.on("route", this.trackPathName);
+
 			// Clear stale JSONLD and meta tags
 			this.on("route", this.clearJSONLD);
 			this.on("route", this.clearHighwirePressMetaTags);
 		},
 
 		//Keep track of navigation movements
 		routeHistory: new Array(),
-		hashHistory: new Array(),
+		pathHistory: new Array(),
 
 		// Will return the last route, which is actually the second to last item in the route history,
 		// since the last item is the route being currently viewed
@@ -58,21 +58,21 @@ function ($, _, Backbone) {
 				return this.routeHistory[this.routeHistory.length-2];
 		},
 
-		trackHash: function(e){
-			if(_.last(this.hashHistory) != window.location.hash)
-				this.hashHistory.push(window.location.hash);
+		trackPathName: function(e){
+			if(_.last(this.pathHistory) != window.location.pathname)
+				this.pathHistory.push(window.location.pathname);
 		},
 
-		//If the user or app cancelled the last route, call this function to revert the window location hash back to the correct value
+		//If the user or app cancelled the last route, call this function to revert the window location pathname back to the correct value
 		undoLastRoute: function(){
 			this.routeHistory.pop();
 
-			//Remove the last route and hash from the history
-			if(_.last(this.hashHistory) == window.location.hash)
-				this.hashHistory.pop();
+			//Remove the last route and pathname from the history
+			if(_.last(this.pathHistory) == window.location.pathname)
+				this.pathHistory.pop();
 
-			//Change the hash in the window location back
-			this.navigate(_.last(this.hashHistory), {replace: true});
+			//Change the pathname in the window location back
+			this.navigate(_.last(this.pathHistory), {replace: true});
 		},
 
 		renderMdqRun: function (suiteId, pid) {
@@ -144,9 +144,9 @@ function ($, _, Backbone) {
 
 			//Check for a query URL parameter
 			if((typeof query !== "undefined") && query){
-				var customQuery = appSearchModel.get('additionalCriteria');
+				var customQuery = MetacatUI.appSearchModel.get('additionalCriteria');
 				customQuery.push(query);
-				appSearchModel.set('additionalCriteria', customQuery);
+				MetacatUI.appSearchModel.set('additionalCriteria', customQuery);
 			}
 
 			if(!MetacatUI.appView.dataCatalogView){
@@ -210,7 +210,7 @@ function ($, _, Backbone) {
 		renderMetadata: function (pid) {
 			this.routeHistory.push("metadata");
 			MetacatUI.appModel.set('lastPid', MetacatUI.appModel.get("pid"));
-			
+
 			var seriesId;
 
 			//Check for a seriesId
@@ -281,7 +281,7 @@ function ($, _, Backbone) {
 					MetacatUI.appView.showView(MetacatUI.appView.userView, viewOptions);
 			}
 		},
-		
+
 		renderMyProfile: function(section, subsection){
 			if(MetacatUI.appUserModel.get("checked") && !MetacatUI.appUserModel.get("loggedIn"))
 				this.renderTokenSignIn();

src/js/themes/dataone/templates/resultsItem.html

@@ -13,7 +13,7 @@
 	<% } %>
 	<div class="resource-map icons stop-route">
 		<% if (resourceMap) {
-				print('<img src="js/themes/dataone/img/data-file-icon-magenta-desat.png" class="icon tooltip-this stop-route"  data-toggle="tooltip" data-placement="top" title="This data set includes data files"></i>');
+				print('<img src="' + MetacatUI.root + '/js/themes/dataone/img/data-file-icon-magenta-desat.png" class="icon tooltip-this stop-route"  data-toggle="tooltip" data-placement="top" title="This data set includes data files"></i>');
 			} %>
 
 	</div>

src/js/themes/goa/routers/router.js

@@ -34,23 +34,23 @@ function ($, _, Backbone) {
 			MetacatUI.appModel.set('ldapwebServiceUrl', 'https://knb.ecoinformatics.org/knb/cgi-bin/ldapweb.cgi');
 
 			this.listenTo(Backbone.history, "routeNotFound", this.navigateToDefault);
-			
+
 			// This route handler replaces the route handler we had in the
 			// routes table before which was "view/*pid". The * only finds URL
 			// parts until the ? but DataONE PIDs can have ? in them so we need
 			// to make this route more inclusive.
 			this.route(/^view\/(.*)$/, "renderMetadata");
 
-			this.on("route", this.trackHash);
-			
+			this.on("route", this.trackPathName);
+
 			// Clear stale JSONLD and meta tags
 			this.on("route", this.clearJSONLD);
 			this.on("route", this.clearHighwirePressMetaTags);
 		},
 
 		//Keep track of navigation movements
 		routeHistory: new Array(),
-		hashHistory: new Array(),
+		pathHistory: new Array(),
 
 		// Will return the last route, which is actually the second to last item in the route history,
 		// since the last item is the route being currently viewed
@@ -61,21 +61,22 @@ function ($, _, Backbone) {
 				return this.routeHistory[this.routeHistory.length-2];
 		},
 
-		trackHash: function(e){
-			if(_.last(this.hashHistory) != window.location.hash)
-				this.hashHistory.push(window.location.hash);
+		trackPathName: function(e){
+			if(_.last(this.pathHistory) != window.location.pathname)
+				this.pathHistory.push(window.location.pathname);
 		},
 
-		//If the user or app cancelled the last route, call this function to revert the window location hash back to the correct value
+		//If the user or app cancelled the last route, call this function to revert
+		// the window location pathname back to the correct value
 		undoLastRoute: function(){
 			this.routeHistory.pop();
 
-			Remove the last route and hash from the history
-			if(_.last(this.hashHistory) == window.location.hash)
-				this.hashHistory.pop();
+			Remove the last route and pathname from the history
+			if(_.last(this.pathHistory) == window.location.pathname)
+				this.pathHistory.pop();
 
-			//Change the hash in the window location back
-			this.navigate(_.last(this.hashHistory), {replace: true});
+			//Change the pathname in the window location back
+			this.navigate(_.last(this.pathHistory), {replace: true});
 		},
 
 		renderText: function(options){