From dfb87ef9f979ef35527770e6dbb7ff1c765ea3a0 Mon Sep 17 00:00:00 2001
From: Dannon Baker <dannon.baker@gmail.com>
Date: Thu, 19 Jan 2023 22:07:12 -0500
Subject: [PATCH] Update, fix ngl visualization

---
 config/plugins/visualizations/ngl/src/ngl.js | 34 ++++++++++++--------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/config/plugins/visualizations/ngl/src/ngl.js b/config/plugins/visualizations/ngl/src/ngl.js
index b9d92f73bec..65dc0c67038 100644
--- a/config/plugins/visualizations/ngl/src/ngl.js
+++ b/config/plugins/visualizations/ngl/src/ngl.js
@@ -1,31 +1,37 @@
 import * as ngl from "./viewer";
 
 /** Get boolean as string */
-function asBoolean (value) {
+function asBoolean(value) {
     return String(value).toLowerCase() == "true";
 }
 
+/* This should be part of the charts/viz standard lib */
+const slashCleanup = /(\/)+/g;
+function prefixedDownloadUrl(root, path) {
+    return `${root}/${path}`.replace(slashCleanup, "/");
+}
+
 window.bundleEntries = window.bundleEntries || {};
 window.bundleEntries.load = function (options) {
-    var dataset = options.dataset,
-        settings = options.chart.settings,
-        stage = new ngl.Stage(options.target, { backgroundColor: settings.get("backcolor") }),
-        representation_parameters = {},
-        stage_parameters = {};
-    representation_parameters = {
+    const dataset = options.dataset;
+    const settings = options.chart.settings;
+    const stage = new ngl.Stage(options.target, { backgroundColor: settings.get("backcolor") });
+    const representationParameters = {
         radius: settings.get("radius"),
         assembly: settings.get("assembly"),
         color: settings.get("colorscheme"),
         opacity: settings.get("opacity"),
     };
-    stage_parameters = { ext: dataset.extension, defaultRepresentation: true };
-    const safe_download_url = `${options.root}${dataset.download_url}`;
+    const stageParameters = { ext: dataset.extension, defaultRepresentation: true };
+
     try {
-        stage.loadFile(safe_download_url, stage_parameters).then(function (component) {
-            component.addRepresentation(settings.get("mode"), representation_parameters);
-            options.chart.state("ok", "Chart drawn.");
-            options.process.resolve();
-        });
+        stage
+            .loadFile(prefixedDownloadUrl(options.root, dataset.download_url), stageParameters)
+            .then(function (component) {
+                component.addRepresentation(settings.get("mode"), representationParameters);
+                options.chart.state("ok", "Chart drawn.");
+                options.process.resolve();
+            });
     } catch (e) {
         options.chart.state("failed", "Could not load PDB file.");
         options.process.resolve();