Cleanup

Remove:
Modernizr, Old JS polyfills
Move venn.js to include as JS
Rename d3.min.js to d3_OLD_VERSION.min.js

proxl_web_app/src/main/webapp/js/libs/venn.js → proxl_web_app/front_end/src/js/libs/venn.js

@@ -1,4 +1,5 @@
 /*
+ * venn.js
  * 
  * Copyright (C) 2013 Ben Frederickson
  * 
@@ -15,6 +16,10 @@
  * 
  * Changes made for Proxl web app:
  * 
+ * Update for ES6 Imports ( Add export )
+ * 
+ * add import * as d3 from "d3";
+ * 
  *  In function:   venn.drawD3Diagram 
  *
  *  After:   var colours = d3.scale.category10();
@@ -30,8 +35,21 @@
  * 
  */
 
+//  import of d3 does not work.    Likely this code does not work with current d3 considering how old this code is.
+
+//   import * as d3 from "d3";
+
+//  This fails:  var colours = d3.scale.category10();
+
+//     Cannot read property 'category10' of undefined
 
-(function(venn) {
+
+
+//(function(venn) {
+
+	const venn = {};
+
+
     "use strict";
     /** given a list of set objects, and their corresponding overlaps.
     updates the (x, y, radius) attribute on each set such that their positions
@@ -608,7 +626,6 @@
 
     venn.drawD3Diagram = function(element, dataset, width, height, parameters) {
 
-
         parameters = parameters || {};
 
         var colours = d3.scale.category10();
@@ -910,4 +927,6 @@
         center.y /= points.length;
         return center;
     };
-}(window.venn = window.venn || {}));
+//}(window.venn = window.venn || {}));
+
+export { venn }

proxl_web_app/front_end/src/js/page_js/data_pages/project_search_ids_driven_pages/common/lorikeetPageProcessing.js

@@ -318,7 +318,7 @@ function addOpenLorikeetViewerClickHandlers( $openLorkeetLinks ) {
 
 			var svgSupportedSnapLoaded = false;
 
-			if ( typeof Modernizr !== 'undefined' && Modernizr.svg && typeof Snap !== 'undefined' ) {
+			if ( typeof Snap !== 'undefined' ) {
 
 				svgSupportedSnapLoaded = true;
 			}
@@ -666,7 +666,7 @@ function addOpenLorikeetViewerClickHandlers( $openLorkeetLinks ) {
 
 				//  END:  Create Text representation of Looplink
 
-			} //  else of if ( Modernizr && Modernizr.svg && Snap ) {
+			} //  else of if ( Snap ) {
 
 		}
 

proxl_web_app/front_end/src/js/page_js/data_pages/project_search_ids_driven_pages/common_merged_pages/mergedSearchesVennDiagramCreator.js

@@ -1,16 +1,18 @@
 
-//mergedSearchesVennDiagramCreator.js
+//  mergedSearchesVennDiagramCreator.js
 
 //JavaScript directive:   all variables have to be declared with "var", maybe other things
 "use strict";
 
-
+import { venn } from 'libs/venn.js';
 
 /**
  * Constructor 
  */
 var CreateMergedSearchesLinkCountsVennDiagram = function() {
 
+	let retryCountOnMissing_d3_Object = 0;
+
 	///////////////////////////////////////////
 	//	This is a copy of colors in CSS classes altered to compensate for fill-opacity: 0.3 in the venn diagram
 	//	CSS class names start with "merged-search-search-background-color-" and are in the file global.css
@@ -24,6 +26,22 @@ var CreateMergedSearchesLinkCountsVennDiagram = function() {
 	///////////////////////////////////////////
 	//	This function is called on the page to create the Venn diagram
 	this.createMergedSearchesLinkCountsVennDiagram = function({ vennDiagramDataToJSON }) {
+
+		if ( ! window.d3 ) {
+			retryCountOnMissing_d3_Object++;
+			//  d3 object not on page yet so try again in 1 second
+			if ( retryCountOnMissing_d3_Object > 1 ) {
+				throw Error("window.d3 not exist");
+			}
+			window.setTimeout( () => {
+				try {
+					this.createMergedSearchesLinkCountsVennDiagram({ vennDiagramDataToJSON });
+				} catch( e ) {
+					reportWebErrorToServer.reportErrorObjectToServer( { errorException : e } );
+					throw e;
+				}
+			}, 1000);
+		}
 		try {
 			var venn_diagram_data = vennDiagramDataToJSON;
 
@@ -51,7 +69,7 @@ var CreateMergedSearchesLinkCountsVennDiagram = function() {
 			//  Apply a stroke width
 			$circle_All.attr("stroke-width","1");
 
-			this.addDownloadClickHandlers();
+			this._addDownloadClickHandlers();
 
 			var $searches_intersection_venn_diagram_outer_container = $("#searches_intersection_venn_diagram_outer_container");
 			$searches_intersection_venn_diagram_outer_container.show();
@@ -69,7 +87,7 @@ var CreateMergedSearchesLinkCountsVennDiagram = function() {
 	 * If the element $chart_outer_container_for_download_jq was dynamically added, need to run to add tool tips on download links: 
 	 *			addToolTips( $chartOuterContainer );
 	 */
-	this.addDownloadClickHandlers = function( params ) {
+	this._addDownloadClickHandlers = function( params ) {
 		var objectThis = this;
 		var $searches_intersection_venn_diagram_outer_container = $("#searches_intersection_venn_diagram_outer_container");
 		var $venn_diagram_download_link_jq_All = $searches_intersection_venn_diagram_outer_container.find(".venn_diagram_download_link_jq");

proxl_web_app/front_end/src/js/page_js/data_pages/project_search_ids_driven_pages/image_page/crosslink-image-viewer.js

@@ -6157,10 +6157,6 @@ var ImagePagePrimaryRootCodeClass = function() {
 		populateAnnotationDataDisplayProcessingCommonCodeFromHash();
 		proteinAnnotationStore.init();
 
-		if ( Modernizr && ! Modernizr.svg ) {  //  Modernizr.svg is false if SVG not supported
-			console.log( "SVG not supported." );
-			throw Error( "SVG not supported" );
-		}
 		_projectSearchIds = [];
 		var $project_search_id_jq = $(".project_search_id_jq");
 		if ( $project_search_id_jq.length === 0 ) {

proxl_web_app/front_end/src/js/page_js/data_pages/project_search_ids_driven_pages/structure_page/structure-viewer-page.js

@@ -6552,11 +6552,6 @@ var StructurePagePrimaryRootCodeClass = function() {
 
 		console.log( "Initializing the page." );
 
-		if ( Modernizr && ! Modernizr.svg ) {  //  Modernizr.svg is false if SVG not supported
-			console.log( "SVG not supported." );
-			throw Error( "SVG not supported" );
-		}
-
 		_projectSearchIds = [];
 
 		var $project_search_id_jq = $(".project_search_id_jq");

proxl_web_app/src/main/webapp/WEB-INF/jsp-includes/head_section_include_every_page.jsp

@@ -25,12 +25,6 @@
 
     <link rel="icon" href="images/favicon.ico" />
 
-	<script type="text/javascript" src="js/libs/modernizr.v2.7.1__custom.39924_min.js"></script>
-
-	<%--
-	<script type="text/javascript" src="js/libs/modernizr.v2.7.1__custom.39924.js"></script>
-	--%>
-
 	<script type="text/javascript" src="js/libs/jquery-1.11.0.min.js"></script>
 <%-- 
 	<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.0/jquery.js"></script>
@@ -62,117 +56,6 @@
 	  var _PROXL_COLOR_LINK_TYPE_UNLINKED = _PROXL_COLOR_SITE_BLUE;
 	  var _PROXL_COLOR_LINK_TYPE_ALL_COMBINED = "#A5A5A5";
 	  
-	  <%--
-	  https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/String/Trim
-	  
-	  // Polyfill for String.trim() 
-	  //  Running the following code before any other code will create trim() if it's not natively available.
-		--%>	  
-	  if (!String.prototype.trim) {
-		  String.prototype.trim = function () {
-		    return this.replace(/^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g, '');
-		  };
-		}
-	  
-	  <%--
-	  https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/isArray
-	  
-	  // Polyfill for Array.isArray() 
-	  //  Running the following code before any other code will create Array.isArray() if it's not natively available.
-		--%>
-	  
-	  if (!Array.isArray) {
-	    Array.isArray = function(arg) {
-	      return Object.prototype.toString.call(arg) === '[object Array]';
-	    };
-	  }
-	  
-
-		<%--
-			https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Date/now
-			
-		  // Polyfill for Date.now() 
-		  //  Running the following code before any other code will create Date.now() if it's not natively available.
-		  //  Date.now()  returns  the milliseconds elapsed since 1 January 1970 00:00:00 UTC up until now as a Number.
-		--%>
-	  
-	  if (!Date.now) {
-		  Date.now = function now() {
-		    return new Date().getTime();
-		  };
-		}
-	  
-	  <%--
-	  	https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Array/forEach
-	  	Polyfill
-	  forEach() was added to the ECMA-262 standard in the 5th edition; as such it may not be present in other implementations of the standard. You can work around this by inserting the following code at the beginning of your scripts, allowing use of forEach() in implementations that don't natively support it. This algorithm is exactly the one specified in ECMA-262, 5th edition, assuming Object and TypeError have their original values and that callback.call() evaluates to the original value of Function.prototype.call().
-
-		// Production steps of ECMA-262, Edition 5, 15.4.4.18
-		// Reference: http://es5.github.io/#x15.4.4.18
-	  
-	  --%>
-if (!Array.prototype.forEach) {
-
-  Array.prototype.forEach = function(callback/*, thisArg*/) {
-
-    var T, k;
-
-    if (this == null) {
-      throw new TypeError('this is null or not defined');
-    }
-
-    // 1. Let O be the result of calling toObject() passing the
-    // |this| value as the argument.
-    var O = Object(this);
-
-    // 2. Let lenValue be the result of calling the Get() internal
-    // method of O with the argument "length".
-    // 3. Let len be toUint32(lenValue).
-    var len = O.length >>> 0;
-
-    // 4. If isCallable(callback) is false, throw a TypeError exception. 
-    // See: http://es5.github.com/#x9.11
-    if (typeof callback !== 'function') {
-      throw new TypeError(callback + ' is not a function');
-    }
-
-    // 5. If thisArg was supplied, let T be thisArg; else let
-    // T be undefined.
-    if (arguments.length > 1) {
-      T = arguments[1];
-    }
-
-    // 6. Let k be 0.
-    k = 0;
-
-    // 7. Repeat while k < len.
-    while (k < len) {
-
-      var kValue;
-
-      // a. Let Pk be ToString(k).
-      //    This is implicit for LHS operands of the in operator.
-      // b. Let kPresent be the result of calling the HasProperty
-      //    internal method of O with argument Pk.
-      //    This step can be combined with c.
-      // c. If kPresent is true, then
-      if (k in O) {
-
-        // i. Let kValue be the result of calling the Get internal
-        // method of O with argument Pk.
-        kValue = O[k];
-
-        // ii. Call the Call internal method of callback with T as
-        // the this value and argument list containing kValue, k, and O.
-        callback.call(T, kValue, k, O);
-      }
-      // d. Increase k by 1.
-      k++;
-    }
-    // 8. return undefined.
-  };
-}	  
-	  
 	</script>	
 
 

proxl_web_app/src/main/webapp/WEB-INF/jsp-includes/header_main.jsp

@@ -51,7 +51,7 @@ response.addHeader("Cache-control", "max-age=0"); // stale right away
 
 <!DOCTYPE html>
 
-<html class="no-js"> <!--  Modernizr will change "no-js" to "js" if Javascript is enabled -->
+<html > 
 
 
 <head>

proxl_web_app/src/main/webapp/WEB-INF/jsp-pages/viewMergedCrosslinkProtein.jsp

@@ -14,8 +14,9 @@
 
  		<script type="text/javascript" src="js/libs/jquery.tablesorter_Modified.js"></script> 
 
-		<script type="text/javascript" src="js/libs/d3.min.js"></script>
-		<script type="text/javascript" src="js/libs/venn.js"></script>
+			<%--  Old version of d3 used in venn.js and mergedSearchesVennDiagramCreator.js
+						to create the Venn Diagram --%>
+		<script type="text/javascript" src="js/libs/d3_OLD_VERSION.min.js"></script>
 
 
 <%--  Start of Lorikeet Core Parts --%>		

proxl_web_app/src/main/webapp/WEB-INF/jsp-pages/viewMergedLooplinkProtein.jsp

@@ -17,8 +17,9 @@
  		<script type="text/javascript" src="js/libs/jquery.tablesorter_Modified.js"></script> 
 		<script type="text/javascript" src="js/libs/jquery.qtip.min.js"></script>
 
-		<script type="text/javascript" src="js/libs/d3.min.js"></script>
-		<script type="text/javascript" src="js/libs/venn.js"></script>
+			<%--  Old version of d3 used in venn.js and mergedSearchesVennDiagramCreator.js
+						to create the Venn Diagram --%>
+		<script type="text/javascript" src="js/libs/d3_OLD_VERSION.min.js"></script>
 
 
 <%--  Start of Lorikeet Core Parts --%>		

proxl_web_app/src/main/webapp/WEB-INF/jsp-pages/viewMergedPeptide.jsp

@@ -19,8 +19,9 @@
  		<script type="text/javascript" src="js/libs/jquery.tablesorter_Modified.js"></script> 
 		<script type="text/javascript" src="js/libs/jquery.qtip.min.js"></script>
 
-		<script type="text/javascript" src="js/libs/d3.min.js"></script>
-		<script type="text/javascript" src="js/libs/venn.js"></script>
+			<%--  Old version of d3 used in venn.js and mergedSearchesVennDiagramCreator.js
+						to create the Venn Diagram --%>
+		<script type="text/javascript" src="js/libs/d3_OLD_VERSION.min.js"></script>
 
 
 <%--  Start of Lorikeet Core Parts --%>		

proxl_web_app/src/main/webapp/WEB-INF/jsp-pages/viewMergedProteinAll.jsp

@@ -18,8 +18,9 @@
  		<script type="text/javascript" src="js/libs/jquery.tablesorter_Modified.js"></script> 
 		<script type="text/javascript" src="js/libs/jquery.qtip.min.js"></script>
 
-		<script type="text/javascript" src="js/libs/d3.min.js"></script>
-		<script type="text/javascript" src="js/libs/venn.js"></script>
+			<%--  Old version of d3 used in venn.js and mergedSearchesVennDiagramCreator.js
+						to create the Venn Diagram --%>
+		<script type="text/javascript" src="js/libs/d3_OLD_VERSION.min.js"></script>
 
 
 <%--  Start of Lorikeet Core Parts --%>