@jbrowse/core 1.5.5 → 1.5.6

package/util/stats.test.js

@@ -1,10 +1,10 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _simpleFeature = _interopRequireDefault(require("@jbrowse/core/util/simpleFeature"));
 
@@ -45,9 +45,9 @@ test('test rectify', function () {
     scoreSumSquares: 14
   }).scoreStdDev).toEqual(1); // calculated from a webapp about sample standard deviations
 });
-test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
+test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee() {
   var ret;
-  return _regenerator.default.wrap(function _callee$(_context) {
+  return _index["default"].wrap(function _callee$(_context) {
     while (1) {
       switch (_context.prev = _context.next) {
         case 0:
@@ -56,21 +56,21 @@ test('scores to stats', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE_
             refName: 'ctgA',
             start: 0,
             end: 2
-          }, (0, _rxjs.from)([new _simpleFeature.default({
+          }, (0, _rxjs.from)([new _simpleFeature["default"]({
             id: 1,
             data: {
               start: 0,
               end: 1,
               score: 1
             }
-          }), new _simpleFeature.default({
+          }), new _simpleFeature["default"]({
             id: 2,
             data: {
               start: 1,
               end: 2,
               score: 2
             }
-          }), new _simpleFeature.default({
+          }), new _simpleFeature["default"]({
             id: 3,
             data: {
               start: 2,
@@ -101,7 +101,7 @@ test('calc per base stats', function () {
     refName: 'ctgA',
     start: 0,
     end: 9
-  }, [new _simpleFeature.default({
+  }, [new _simpleFeature["default"]({
     id: 1,
     data: {
       start: 0,
@@ -114,14 +114,14 @@ test('calc per base stats', function () {
     refName: 'ctgA',
     start: 0,
     end: 9
-  }, [new _simpleFeature.default({
+  }, [new _simpleFeature["default"]({
     id: 1,
     data: {
       start: 0,
       end: 1,
       score: 10
     }
-  }), new _simpleFeature.default({
+  }), new _simpleFeature["default"]({
     id: 2,
     data: {
       start: 8,
@@ -134,14 +134,14 @@ test('calc per base stats', function () {
     refName: 'ctgA',
     start: 15,
     end: 30
-  }, [new _simpleFeature.default({
+  }, [new _simpleFeature["default"]({
     id: 1,
     data: {
       start: 10,
       end: 20,
       score: 10
     }
-  }), new _simpleFeature.default({
+  }), new _simpleFeature["default"]({
     id: 2,
     data: {
       start: 25,
@@ -154,14 +154,14 @@ test('calc per base stats', function () {
     refName: 'ctgA',
     start: 10,
     end: 19
-  }, [new _simpleFeature.default({
+  }, [new _simpleFeature["default"]({
     id: 1,
     data: {
       start: 5,
       end: 15,
       score: 10
     }
-  }), new _simpleFeature.default({
+  }), new _simpleFeature["default"]({
     id: 1,
     data: {
       start: 18,

package/util/types/index.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -43,21 +43,19 @@ exports.isUriLocation = isUriLocation;
 exports.isViewContainer = isViewContainer;
 exports.isViewModel = isViewModel;
 
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
+var _createClass2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createClass.js"));
 
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
+var _classCallCheck2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/classCallCheck.js"));
 
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
+var _assertThisInitialized2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/assertThisInitialized.js"));
 
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
+var _inherits2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/inherits.js"));
 
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
+var _createSuper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/createSuper.js"));
 
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
+var _wrapNativeSuper2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/wrapNativeSuper.js"));
 
-var _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime/helpers/wrapNativeSuper"));
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
+var _typeof2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/typeof.js"));
 
 var _mobxStateTree = require("mobx-state-tree");
 
@@ -75,16 +73,12 @@ Object.keys(_util).forEach(function (key) {
   });
 });
 
-function _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = (0, _getPrototypeOf2.default)(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = (0, _getPrototypeOf2.default)(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return (0, _possibleConstructorReturn2.default)(this, result); }; }
-
-function _isNativeReflectConstruct() { if (typeof Reflect === "undefined" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === "function") return true; try { Boolean.prototype.valueOf.call(Reflect.construct(Boolean, [], function () {})); return true; } catch (e) { return false; } }
-
 function isViewContainer(thing) {
   return (0, _mobxStateTree.isStateTreeNode)(thing) && 'removeView' in thing && 'addView' in thing && 'views' in thing;
 }
 
 function isSessionModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'rpcManager' in thing && 'configuration' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'rpcManager' in thing && 'configuration' in thing;
 }
 /** abstract interface for a session allows editing configurations */
 
@@ -110,39 +104,39 @@ function isSessionWithSessionPlugins(thing) {
 
 
 function isSelectionContainer(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'selection' in thing && 'setSelection' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'selection' in thing && 'setSelection' in thing;
 }
 /** minimum interface that all view state models must implement */
 
 
 function isViewModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'width' in thing && 'setWidth' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'width' in thing && 'setWidth' in thing;
 }
 
 function isTrackModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
   thing.configuration.trackId;
 }
 
 function isDisplayModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'configuration' in thing && // @ts-ignore
   thing.configuration.displayId;
 }
 
 function isTrackViewModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'showTrack' in thing && 'hideTrack' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'showTrack' in thing && 'hideTrack' in thing;
 }
 /** minimum interface for the root MST model of a JBrowse app */
 
 
 function isAppRootModel(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'isAssemblyEditing' in thing && 'findAppropriateInternetAccount' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'isAssemblyEditing' in thing && 'findAppropriateInternetAccount' in thing;
 }
 /** a root model that manages global menus */
 
 
 function isAbstractMenuManager(thing) {
-  return (0, _typeof2.default)(thing) === 'object' && thing !== null && 'appendMenu' in thing && 'appendToSubMenu' in thing;
+  return (0, _typeof2["default"])(thing) === 'object' && thing !== null && 'appendMenu' in thing && 'appendToSubMenu' in thing;
 } // Empty interfaces required by mobx-state-tree
 // See https://mobx-state-tree.js.org/tips/typescript#using-a-mst-type-at-design-time
 
@@ -150,45 +144,49 @@ function isAbstractMenuManager(thing) {
 
 
 function isUriLocation(location) {
-  return (0, _typeof2.default)(location) === 'object' && location !== null && 'locationType' in location && 'uri' in location;
+  return (0, _typeof2["default"])(location) === 'object' && location !== null && 'locationType' in location && 'uri' in location;
 }
 
 var AuthNeededError = /*#__PURE__*/function (_Error) {
-  (0, _inherits2.default)(AuthNeededError, _Error);
+  (0, _inherits2["default"])(AuthNeededError, _Error);
 
-  var _super = _createSuper(AuthNeededError);
+  var _super = (0, _createSuper2["default"])(AuthNeededError);
 
   function AuthNeededError(message, location) {
     var _this;
 
-    (0, _classCallCheck2.default)(this, AuthNeededError);
+    (0, _classCallCheck2["default"])(this, AuthNeededError);
     _this = _super.call(this, message);
+    _this.message = message;
+    _this.location = location;
     _this.name = 'AuthNeededError';
-    Object.setPrototypeOf((0, _assertThisInitialized2.default)(_this), AuthNeededError.prototype);
+    Object.setPrototypeOf((0, _assertThisInitialized2["default"])(_this), AuthNeededError.prototype);
     return _this;
   }
 
-  return (0, _createClass2.default)(AuthNeededError);
-}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
+  return (0, _createClass2["default"])(AuthNeededError);
+}( /*#__PURE__*/(0, _wrapNativeSuper2["default"])(Error));
 
 exports.AuthNeededError = AuthNeededError;
 
 var RetryError = /*#__PURE__*/function (_Error2) {
-  (0, _inherits2.default)(RetryError, _Error2);
+  (0, _inherits2["default"])(RetryError, _Error2);
 
-  var _super2 = _createSuper(RetryError);
+  var _super2 = (0, _createSuper2["default"])(RetryError);
 
   function RetryError(message, internetAccountId) {
     var _this2;
 
-    (0, _classCallCheck2.default)(this, RetryError);
+    (0, _classCallCheck2["default"])(this, RetryError);
     _this2 = _super2.call(this, message);
+    _this2.message = message;
+    _this2.internetAccountId = internetAccountId;
     _this2.name = 'RetryError';
     return _this2;
   }
 
-  return (0, _createClass2.default)(RetryError);
-}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
+  return (0, _createClass2["default"])(RetryError);
+}( /*#__PURE__*/(0, _wrapNativeSuper2["default"])(Error));
 
 exports.RetryError = RetryError;
 

package/util/types/mst.js

@@ -1,15 +1,15 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
 });
 exports.UriLocationRaw = exports.UriLocation = exports.Region = exports.PropTypes = exports.NoAssemblyRegion = exports.LocalPathLocation = exports.FileLocation = exports.ElementId = exports.BlobLocation = void 0;
 
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
+var _objectSpread2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectSpread2.js"));
 
-var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
+var _objectWithoutProperties2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/objectWithoutProperties.js"));
 
 var _shortid = _interopRequireDefault(require("shortid"));
 
@@ -22,24 +22,20 @@ var _mobxReact = require("mobx-react");
 var _excluded = ["baseUri"],
     _excluded2 = ["locationType"];
 
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-var ElementId = _mobxStateTree.types.optional(_mobxStateTree.types.identifier, _shortid.default.generate); // PropTypes that are useful when working with instances of these in react components
+var ElementId = _mobxStateTree.types.optional(_mobxStateTree.types.identifier, _shortid["default"].generate); // PropTypes that are useful when working with instances of these in react components
 
 
 exports.ElementId = ElementId;
 var PropTypes = {
-  Region: _propTypes.default.shape({
-    refName: _propTypes.default.string.isRequired,
-    start: _propTypes.default.number.isRequired,
-    end: _propTypes.default.number.isRequired
+  Region: _propTypes["default"].shape({
+    refName: _propTypes["default"].string.isRequired,
+    start: _propTypes["default"].number.isRequired,
+    end: _propTypes["default"].number.isRequired
   }),
   ConfigSchema: _mobxReact.PropTypes.objectOrObservableObject,
-  Feature: _propTypes.default.shape({
-    get: _propTypes.default.func.isRequired,
-    id: _propTypes.default.func.isRequired
+  Feature: _propTypes["default"].shape({
+    get: _propTypes["default"].func.isRequired,
+    id: _propTypes["default"].func.isRequired
   })
 };
 exports.PropTypes = PropTypes;
@@ -48,7 +44,7 @@ var NoAssemblyRegion = _mobxStateTree.types.model('NoAssemblyRegion', {
   refName: _mobxStateTree.types.string,
   start: _mobxStateTree.types.number,
   end: _mobxStateTree.types.number,
-  reversed: _mobxStateTree.types.optional(_mobxStateTree.types.boolean, false)
+  reversed: _mobxStateTree.types.optional(_mobxStateTree.types["boolean"], false)
 }).actions(function (self) {
   return {
     setRefName: function setRefName(newRefName) {
@@ -99,7 +95,7 @@ exports.UriLocationRaw = UriLocationRaw;
 var UriLocation = _mobxStateTree.types.snapshotProcessor(UriLocationRaw, {
   postProcessor: function postProcessor(snap) {
     var baseUri = snap.baseUri,
-        rest = (0, _objectWithoutProperties2.default)(snap, _excluded);
+        rest = (0, _objectWithoutProperties2["default"])(snap, _excluded);
 
     if (!baseUri) {
       return rest;
@@ -120,7 +116,7 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
 
 
     var locationType = snapshot.locationType,
-        rest = (0, _objectWithoutProperties2.default)(snapshot, _excluded2);
+        rest = (0, _objectWithoutProperties2["default"])(snapshot, _excluded2);
 
     if (!locationType) {
       // @ts-ignore
@@ -137,7 +133,7 @@ var FileLocation = _mobxStateTree.types.snapshotProcessor(_mobxStateTree.types.u
         _locationType = 'BlobLocation';
       }
 
-      return _objectSpread(_objectSpread({}, rest), {}, {
+      return (0, _objectSpread2["default"])((0, _objectSpread2["default"])({}, rest), {}, {
         locationType: _locationType
       });
     }

package/util/types/util.js

@@ -1 +1,5 @@
-"use strict";
+"use strict";
+
+Object.defineProperty(exports, "__esModule", {
+  value: true
+});

package/util/when.js

@@ -1,6 +1,6 @@
 "use strict";
 
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
+var _interopRequireDefault = require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/interopRequireDefault.js")["default"];
 
 Object.defineProperty(exports, "__esModule", {
   value: true
@@ -8,9 +8,9 @@ Object.defineProperty(exports, "__esModule", {
 exports.when = when;
 exports.whenPresent = whenPresent;
 
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
+var _index = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/regenerator/index.js"));
 
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
+var _asyncToGenerator2 = _interopRequireDefault(require("/home/ubuntu/jbrowse-components/node_modules/@babel/runtime/helpers/esm/asyncToGenerator.js"));
 
 var _mobx = require("mobx");
 
@@ -66,7 +66,7 @@ function when(getter) {
         finishTimeout();
         resolve(true);
       }
-    }).catch(function (err) {
+    })["catch"](function (err) {
       if (!finished) {
         finished = true;
         finishTimeout();
@@ -87,10 +87,10 @@ function whenPresent(_x) {
 }
 
 function _whenPresent() {
-  _whenPresent = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(getter) {
+  _whenPresent = (0, _asyncToGenerator2["default"])( /*#__PURE__*/_index["default"].mark(function _callee(getter) {
     var opts,
         _args = arguments;
-    return _regenerator.default.wrap(function _callee$(_context) {
+    return _index["default"].wrap(function _callee$(_context) {
       while (1) {
         switch (_context.prev = _context.next) {
           case 0:

package/babel.config.d.ts

@@ -1,15 +0,0 @@
-declare function _exports(api: any): {
-    babelrcRoots: string[];
-    comments: boolean;
-    presets: (string | (string | {
-        targets: {
-            node: number;
-            browsers: string[];
-        };
-    })[])[];
-    ignore: string[];
-    plugins: (string | (string | {
-        useESModules: boolean;
-    })[])[];
-};
-export = _exports;

package/babel.config.js

@@ -1,19 +0,0 @@
-"use strict";
-
-module.exports = function (api) {
-  api.cache(false);
-  return {
-    babelrcRoots: ['.', './packages/*', './products/*', './plugins/*'],
-    comments: true,
-    presets: ['@babel/preset-typescript', '@babel/preset-react', ['@babel/preset-env', {
-      targets: {
-        node: 8,
-        browsers: ['> 0.5%', 'last 2 versions']
-      }
-    }]],
-    ignore: ['./node_modules', './packages/*/node_modules', './products/*/node_modules', './plugins/*/node_modules'],
-    plugins: ['@babel/plugin-syntax-dynamic-import', '@babel/plugin-proposal-class-properties', '@babel/plugin-proposal-export-default-from', ['@babel/transform-runtime', {
-      useESModules: false
-    }], 'inline-import-data-uri']
-  };
-};