@jbrowse/core 1.6.7 → 1.7.0

package/BaseFeatureWidget/BaseFeatureDetail.d.ts

@@ -39,8 +39,8 @@ export interface BaseInputProps extends BaseCardProps {
 export declare const FeatureDetails: (props: {
     model: IAnyStateTreeNode;
     feature: SimpleFeatureSerialized & {
-        name?: string | undefined;
-        id?: string | undefined;
+        name?: string;
+        id?: string;
     };
     depth?: number | undefined;
     omit?: string[] | undefined;

package/PluginLoader.d.ts

@@ -28,14 +28,22 @@ export interface LoadedPlugin {
 }
 export default class PluginLoader {
     definitions: PluginDefinition[];
-    constructor(pluginDefinitions?: PluginDefinition[]);
+    fetchESM?: (url: string) => Promise<unknown>;
+    fetchCJS?: (url: string) => Promise<LoadedPlugin>;
+    constructor(pluginDefinitions?: PluginDefinition[], args?: {
+        fetchESM?: (url: string) => Promise<unknown>;
+        fetchCJS?: (url: string) => Promise<LoadedPlugin>;
+    });
     loadScript(scriptUrl: string): Promise<void>;
-    loadCJSPlugin(pluginDefinition: CJSPluginDefinition): Promise<LoadedPlugin>;
+    loadCJSPlugin({ cjsUrl }: CJSPluginDefinition): Promise<LoadedPlugin>;
     loadESMPlugin(pluginDefinition: ESMPluginDefinition): Promise<LoadedPlugin>;
     loadUMDPlugin(pluginDefinition: UMDPluginDefinition | LegacyUMDPluginDefinition): Promise<{
         default: PluginConstructor;
     }>;
     loadPlugin(definition: PluginDefinition): Promise<PluginConstructor>;
     installGlobalReExports(target: WindowOrWorkerGlobalScope): void;
-    load(): Promise<PluginRecord[]>;
+    load(): Promise<{
+        plugin: PluginConstructor;
+        definition: PluginDefinition;
+    }[]>;
 }

package/PluginLoader.js

@@ -2,8 +2,6 @@
 
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-var _typeof3 = require("@babel/runtime/helpers/typeof");
-
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
@@ -28,18 +26,12 @@ var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
 
 var _loadScript = _interopRequireDefault(require("load-script2"));
 
-var _sanitizeFilename = _interopRequireDefault(require("sanitize-filename"));
-
 var _configuration = require("./configuration");
 
 var _ReExports = _interopRequireDefault(require("./ReExports"));
 
 var _util = require("./util");
 
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof3(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
 var PluginSourceConfigurationSchema = (0, _configuration.ConfigurationSchema)('PluginSource', {
   name: {
     type: 'string',
@@ -67,8 +59,7 @@ function isCJSPluginDefinition(pluginDefinition) {
 function getGlobalObject() {
   // Based on window-or-global
   // https://github.com/purposeindustries/window-or-global/blob/322abc71de0010c9e5d9d0729df40959e1ef8775/lib/index.js
-  return (
-    /* eslint-disable-next-line no-restricted-globals */
+  return (// eslint-disable-next-line no-restricted-globals
     (typeof self === "undefined" ? "undefined" : (0, _typeof2.default)(self)) === 'object' && self.self === self && self || (typeof global === "undefined" ? "undefined" : (0, _typeof2.default)(global)) === 'object' && global.global === global && global || // @ts-ignore
     this
   );
@@ -81,8 +72,13 @@ function isInWebWorker(globalObject) {
 var PluginLoader = /*#__PURE__*/function () {
   function PluginLoader() {
     var pluginDefinitions = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : [];
+    var args = arguments.length > 1 ? arguments[1] : undefined;
     (0, _classCallCheck2.default)(this, PluginLoader);
     (0, _defineProperty2.default)(this, "definitions", []);
+    (0, _defineProperty2.default)(this, "fetchESM", void 0);
+    (0, _defineProperty2.default)(this, "fetchCJS", void 0);
+    this.fetchESM = args === null || args === void 0 ? void 0 : args.fetchESM;
+    this.fetchCJS = args === null || args === void 0 ? void 0 : args.fetchCJS;
     this.definitions = JSON.parse(JSON.stringify(pluginDefinitions));
   }
 
@@ -115,95 +111,49 @@ var PluginLoader = /*#__PURE__*/function () {
   }, {
     key: "loadCJSPlugin",
     value: function () {
-      var _loadCJSPlugin = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(pluginDefinition) {
-        var parsedUrl, fs, path, os, http, fsPromises, systemTmp, tmpDir, plugin, pluginLocation, pluginLocationRelative, pluginDownload;
+      var _loadCJSPlugin = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(_ref) {
+        var cjsUrl, parsedUrl;
         return _regenerator.default.wrap(function _callee$(_context) {
           while (1) {
             switch (_context.prev = _context.next) {
               case 0:
-                _context.prev = 0;
-                parsedUrl = new URL(pluginDefinition.cjsUrl, getGlobalObject().location.href);
-                _context.next = 8;
+                cjsUrl = _ref.cjsUrl;
+                _context.prev = 1;
+                parsedUrl = new URL(cjsUrl, getGlobalObject().location.href);
+                _context.next = 9;
                 break;
 
-              case 4:
-                _context.prev = 4;
-                _context.t0 = _context["catch"](0);
+              case 5:
+                _context.prev = 5;
+                _context.t0 = _context["catch"](1);
                 console.error(_context.t0);
-                throw new Error("Error parsing URL: ".concat(pluginDefinition.cjsUrl));
+                throw new Error("Error parsing URL: ".concat(cjsUrl));
 
-              case 8:
+              case 9:
                 if (!(parsedUrl.protocol !== 'http:' && parsedUrl.protocol !== 'https:')) {
-                  _context.next = 10;
+                  _context.next = 11;
                   break;
                 }
 
-                throw new Error("cannot load plugins using protocol \"".concat(parsedUrl.protocol, "\""));
-
-              case 10:
-                fs = require('fs');
-                path = require('path');
-                os = require('os');
-                http = require('http');
-                fsPromises = fs.promises; // On macOS `os.tmpdir()` returns the path to a symlink, see:
-                // https://github.com/nodejs/node/issues/11422
-
-                _context.next = 17;
-                return fsPromises.realpath(os.tmpdir());
+                throw new Error("Cannot load plugins using protocol \"".concat(parsedUrl.protocol, "\""));
 
-              case 17:
-                systemTmp = _context.sent;
-                _context.next = 20;
-                return fsPromises.mkdtemp(path.join(systemTmp, 'jbrowse-plugin-'));
-
-              case 20:
-                tmpDir = _context.sent;
-                plugin = undefined;
-                _context.prev = 22;
-                pluginLocation = path.join(tmpDir, (0, _sanitizeFilename.default)(parsedUrl.href));
-                pluginLocationRelative = path.relative('.', pluginLocation);
-                pluginDownload = new Promise(function (resolve, reject) {
-                  var file = fs.createWriteStream(pluginLocation);
-                  http.get(parsedUrl.href, function (response) {
-                    response.pipe(file);
-                    file.on('finish', function () {
-                      resolve();
-                    });
-                  }).on('error', function (err) {
-                    fs.unlinkSync(pluginLocation);
-                    reject(err);
-                  });
-                });
-                _context.next = 28;
-                return pluginDownload;
-
-              case 28:
-                plugin = __non_webpack_require__(pluginLocationRelative);
-
-              case 29:
-                _context.prev = 29;
-                fsPromises.rmdir(tmpDir, {
-                  recursive: true
-                });
-                return _context.finish(29);
-
-              case 32:
-                if (plugin) {
-                  _context.next = 34;
+              case 11:
+                if (this.fetchCJS) {
+                  _context.next = 13;
                   break;
                 }
 
-                throw new Error("Could not load CJS plugin: ".concat(parsedUrl));
+                throw new Error('No fetchCJS callback provided');
 
-              case 34:
-                return _context.abrupt("return", plugin);
+              case 13:
+                return _context.abrupt("return", this.fetchCJS(parsedUrl.href));
 
-              case 35:
+              case 14:
               case "end":
                 return _context.stop();
             }
           }
-        }, _callee, null, [[0, 4], [22,, 29, 32]]);
+        }, _callee, this, [[1, 5]]);
       }));
 
       function loadCJSPlugin(_x) {
@@ -216,6 +166,8 @@ var PluginLoader = /*#__PURE__*/function () {
     key: "loadESMPlugin",
     value: function () {
       var _loadESMPlugin = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(pluginDefinition) {
+        var _this$fetchESM;
+
         var parsedUrl, plugin;
         return _regenerator.default.wrap(function _callee2$(_context2) {
           while (1) {
@@ -242,11 +194,7 @@ var PluginLoader = /*#__PURE__*/function () {
 
               case 10:
                 _context2.next = 12;
-                return Promise.resolve("".concat(
-                /* webpackIgnore: true */
-                parsedUrl.href)).then(function (s) {
-                  return _interopRequireWildcard(require(s));
-                });
+                return (_this$fetchESM = this.fetchESM) === null || _this$fetchESM === void 0 ? void 0 : _this$fetchESM.call(this, parsedUrl.href);
 
               case 12:
                 plugin = _context2.sent;
@@ -266,7 +214,7 @@ var PluginLoader = /*#__PURE__*/function () {
                 return _context2.stop();
             }
           }
-        }, _callee2, null, [[0, 4]]);
+        }, _callee2, this, [[0, 4]]);
       }));
 
       function loadESMPlugin(_x2) {
@@ -421,10 +369,10 @@ var PluginLoader = /*#__PURE__*/function () {
     key: "installGlobalReExports",
     value: function installGlobalReExports(target) {
       // @ts-ignore
-      target.JBrowseExports = Object.fromEntries(Object.entries(_ReExports.default).map(function (_ref) {
-        var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-            moduleName = _ref2[0],
-            module = _ref2[1];
+      target.JBrowseExports = Object.fromEntries(Object.entries(_ReExports.default).map(function (_ref2) {
+        var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
+            moduleName = _ref3[0],
+            module = _ref3[1];
 
         return [moduleName, module];
       }));
@@ -440,7 +388,7 @@ var PluginLoader = /*#__PURE__*/function () {
             switch (_context6.prev = _context6.next) {
               case 0:
                 return _context6.abrupt("return", Promise.all(this.definitions.map( /*#__PURE__*/function () {
-                  var _ref3 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(definition) {
+                  var _ref4 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(definition) {
                     return _regenerator.default.wrap(function _callee5$(_context5) {
                       while (1) {
                         switch (_context5.prev = _context5.next) {
@@ -465,7 +413,7 @@ var PluginLoader = /*#__PURE__*/function () {
                   }));
 
                   return function (_x5) {
-                    return _ref3.apply(this, arguments);
+                    return _ref4.apply(this, arguments);
                   };
                 }())));
 

package/PluginManager.d.ts

@@ -221,7 +221,7 @@ export default class PluginManager {
             interRegionPaddingWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
             minimumBlockWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
         }, {
-            features: import("./util/simpleFeature").Feature[] | undefined;
+            features: import("./util").Feature[] | undefined;
             volatileWidth: number;
         } & {
             setDisplayedRegions(regions: import("./util").Region[]): void;
@@ -264,7 +264,7 @@ export default class PluginManager {
                 regionNumber?: number | undefined;
             }): number | undefined;
         } & {
-            setFeatures(features: import("./util/simpleFeature").Feature[]): void;
+            setFeatures(features: import("./util").Feature[]): void;
             zoomToDisplayedRegions(leftPx: import("./util/Base1DViewModel").BpOffset | undefined, rightPx: import("./util/Base1DViewModel").BpOffset | undefined): void;
             showAllRegions(): void;
             moveTo(start: import("./util/Base1DViewModel").BpOffset, end: import("./util/Base1DViewModel").BpOffset): void;

package/PluginManager.js

@@ -96,13 +96,11 @@ var PhasedScheduler = /*#__PURE__*/function () {
       var _this = this;
 
       this.phaseOrder.forEach(function (phaseName) {
-        var phaseCallbacks = _this.phaseCallbacks.get(phaseName);
+        var _this$phaseCallbacks$;
 
-        if (phaseCallbacks) {
-          phaseCallbacks.forEach(function (callback) {
-            return callback();
-          });
-        }
+        (_this$phaseCallbacks$ = _this.phaseCallbacks.get(phaseName)) === null || _this$phaseCallbacks$ === void 0 ? void 0 : _this$phaseCallbacks$.forEach(function (callback) {
+          return callback();
+        });
       });
     }
   }]);

package/ReExports/modules.d.ts

@@ -149,7 +149,7 @@ declare const libs: {
         interRegionPaddingWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
         minimumBlockWidth: mst.IOptionalIType<mst.ISimpleType<number>, [undefined]>;
     }, {
-        features: import("../util/simpleFeature").Feature[] | undefined;
+        features: coreUtil.Feature[] | undefined;
         volatileWidth: number;
     } & {
         setDisplayedRegions(regions: coreUtil.Region[]): void;
@@ -192,7 +192,7 @@ declare const libs: {
             regionNumber?: number | undefined;
         }): number | undefined;
     } & {
-        setFeatures(features: import("../util/simpleFeature").Feature[]): void;
+        setFeatures(features: coreUtil.Feature[]): void;
         zoomToDisplayedRegions(leftPx: import("../util/Base1DViewModel").BpOffset | undefined, rightPx: import("../util/Base1DViewModel").BpOffset | undefined): void;
         showAllRegions(): void;
         moveTo(start: import("../util/Base1DViewModel").BpOffset, end: import("../util/Base1DViewModel").BpOffset): void;

package/assemblyManager/assemblyManager.d.ts

@@ -9,7 +9,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -31,14 +31,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -65,7 +65,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -87,14 +87,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -119,7 +119,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -141,14 +141,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -184,7 +184,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -206,14 +206,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -238,7 +238,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -260,14 +260,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -307,7 +307,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -329,14 +329,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{
@@ -361,7 +361,7 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
         refNameAliases: {
             [key: string]: string;
         } | undefined;
-        cytobands: import("../util/simpleFeature").Feature[] | undefined;
+        cytobands: import("../util").Feature[] | undefined;
     } & {
         readonly initialized: boolean;
         readonly name: string;
@@ -383,14 +383,14 @@ export default function assemblyManagerFactory(assemblyConfigType: IAnyType, plu
             refNameAliases: {
                 [x: string]: string;
             };
-            cytobands: import("../util/simpleFeature").Feature[];
+            cytobands: import("../util").Feature[];
         }): void;
         setError(e: Error): void;
         setRegions(regions: import("../util").Region[]): void;
         setRefNameAliases(refNameAliases: {
             [x: string]: string;
         }): void;
-        setCytobands(cytobands: import("../util/simpleFeature").Feature[]): void;
+        setCytobands(cytobands: import("../util").Feature[]): void;
         afterAttach(): void;
     } & {
         getAdapterMapEntry(adapterConf: unknown, options: import("./assembly").BaseOptions): Promise<{

package/configuration/util.js

@@ -89,11 +89,7 @@ function readConfObject(confObject) {
       subConf = confObject.get(slotName);
     }
 
-    if (!subConf) {
-      return undefined;
-    }
-
-    return readConfObject(subConf, newPath, args);
+    return subConf ? readConfObject(subConf, newPath, args) : undefined;
   }
 
   return readConfObject(confObject, slotName, args);