Fix PV Protein Viewer build

client/gulpfile.js

@@ -18,6 +18,7 @@ const PLUGIN_BUILD_DIRS = [
     "media_player",
     "mvpapp",
     "openlayers",
+    "pv",
 ];
 
 const paths = {

config/plugins/visualizations/pv/package.json

@@ -10,10 +10,11 @@
     "dependencies": {
         "babel-preset-env": "^1.6.1",
         "backbone": "^1.3.3",
+        "bio-pv": "^1.8.1",
         "bootstrap": "^3.3.7",
-        "jquery": "^3.1.1",
+        "jquery": "^3.5.1",
         "parcel-bundler": "^1.4.1",
-        "bio-pv": "^1.8.1"
+        "underscore": "^1.11.0"
     },
     "scripts": {
         "build": "parcel build src/pv.js -d static"

config/plugins/visualizations/pv/src/pv.js

@@ -1,35 +1,40 @@
 import * as pv from "bio-pv";
+import _ from "underscore";
+import $ from "jquery";
+
 _.extend(window.bundleEntries || {}, {
-    load: function(options) {
+    load: function (options) {
         var settings = options.chart.settings;
         var viewer = pv.Viewer(document.getElementById(options.targets[0]), {
-            quality: settings.get('quality'),
-            width: 'auto',
-            height: 'auto',
+            quality: settings.get("quality"),
+            width: "auto",
+            height: "auto",
             antialias: true,
-            outline: true
+            outline: true,
         });
-        $.ajax( {
+        $.ajax({
             url: options.dataset.download_url,
             cache: true,
-            success: function(response) {
+            success: function (response) {
                 var structure = pv.io.pdb(response);
                 var viewer_options = {};
-                _.each(settings.attributes, function(value, key) {
-                    viewer_options[key.replace('viewer|', '')] = value;
+                _.each(settings.attributes, function (value, key) {
+                    viewer_options[key.replace("viewer|", "")] = value;
                 });
                 viewer.clear();
-                viewer.renderAs('protein', structure, viewer_options.mode, viewer_options);
+                viewer.renderAs("protein", structure, viewer_options.mode, viewer_options);
                 viewer.centerOn(structure);
                 viewer.autoZoom();
-                options.chart.state('ok', 'Chart drawn.');
+                options.chart.state("ok", "Chart drawn.");
                 options.process.resolve();
             },
-            error: function() {
-                options.chart.state('ok', 'Failed to load pdb file.');
+            error: function () {
+                options.chart.state("ok", "Failed to load pdb file.");
                 options.process.resolve();
-            }
+            },
         });
-        $(window).resize(function() { viewer.fitParent() });
-    }
+        $(window).resize(function () {
+            viewer.fitParent();
+        });
+    },
 });