@jbrowse/plugin-legacy-jbrowse 1.7.10 → 2.0.1

package/dist/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,555 +1,441 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.createFinalConfig = createFinalConfig;
-exports.fetchConfigFile = fetchConfigFile;
-exports.fetchJb1 = fetchJb1;
-exports.parseJb1 = parseJb1;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _io = require("@jbrowse/core/util/io");
-
-var _jb1ConfigParse = require("./jb1ConfigParse");
-
-var _util = require("./util");
-
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __generator = (this && this.__generator) || function (thisArg, body) {
+    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
+    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
+    function verb(n) { return function (v) { return step([n, v]); }; }
+    function step(op) {
+        if (f) throw new TypeError("Generator is already executing.");
+        while (_) try {
+            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
+            if (y = 0, t) op = [op[0] & 2, t.value];
+            switch (op[0]) {
+                case 0: case 1: t = op; break;
+                case 4: _.label++; return { value: op[1], done: false };
+                case 5: _.label++; y = op[1]; op = [0]; continue;
+                case 7: op = _.ops.pop(); _.trys.pop(); continue;
+                default:
+                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
+                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
+                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
+                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
+                    if (t[2]) _.ops.pop();
+                    _.trys.pop(); continue;
+            }
+            op = body.call(thisArg, _);
+        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
+        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
+    }
+};
+var __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.parseJb1 = exports.fetchConfigFile = exports.createFinalConfig = exports.fetchJb1 = void 0;
+var io_1 = require("@jbrowse/core/util/io");
+var jb1ConfigParse_1 = require("./jb1ConfigParse");
+var util_1 = require("./util");
 function isUriLocation(location) {
-  return location.uri !== undefined;
+    return location.uri !== undefined;
 }
-
 function isLocalPathLocation(location) {
-  return location.localPath !== undefined;
+    return location.localPath !== undefined;
 }
-
-function fetchJb1() {
-  return _fetchJb.apply(this, arguments);
-}
-
-function _fetchJb() {
-  _fetchJb = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-    var dataRoot,
-        baseConfig,
-        baseConfigRoot,
-        protocol,
-        dataRootReg,
-        dataRootLocation,
-        baseProtocol,
-        baseConfigLocation,
-        _newConfig,
-        _i3,
-        _arr,
-        conf,
-        fetchedConfig,
-        newConfig,
-        _args = arguments;
-
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            dataRoot = _args.length > 0 && _args[0] !== undefined ? _args[0] : {
-              uri: '',
-              locationType: 'UriLocation'
-            };
-            baseConfig = _args.length > 1 && _args[1] !== undefined ? _args[1] : {
-              include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf']
-            };
-            baseConfigRoot = _args.length > 2 && _args[2] !== undefined ? _args[2] : {
-              uri: '',
-              locationType: 'UriLocation'
-            };
-            protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
-            dataRootReg = JSON.parse(JSON.stringify(dataRoot));
-            dataRootLocation = '';
-
-            if (isUriLocation(dataRoot)) {
-              dataRootLocation = dataRoot.uri;
-            }
-
-            if (isLocalPathLocation(dataRoot)) {
-              dataRootLocation = dataRoot.localPath;
-            }
-
-            if (dataRootLocation.endsWith('/')) {
-              dataRootReg[protocol] = dataRootLocation.slice(0, dataRootLocation.length - 1);
-            }
-
-            if (!(isUriLocation(baseConfigRoot) && baseConfigRoot.uri || isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)) {
-              _context.next = 35;
-              break;
-            }
-
-            baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath';
-            baseConfigLocation = '';
-
-            if (isUriLocation(baseConfigRoot)) {
-              baseConfigLocation = baseConfigRoot.uri;
-            }
-
-            if (isLocalPathLocation(baseConfigRoot)) {
-              baseConfigLocation = baseConfigRoot.localPath;
-            }
-
-            if (baseConfigLocation.endsWith('/')) {
-              baseConfigLocation = baseConfigLocation.slice(0, baseConfigLocation.length - 1);
-            }
-
-            _newConfig = {};
-            _i3 = 0, _arr = ['jbrowse.conf', 'jbrowse_conf.json'];
-
-          case 17:
-            if (!(_i3 < _arr.length)) {
-              _context.next = 33;
-              break;
-            }
-
-            conf = _arr[_i3];
-            fetchedConfig = null;
-            _context.prev = 20;
-            _context.next = 23;
-            return fetchConfigFile((0, _defineProperty2.default)({}, baseProtocol, "".concat(baseConfigLocation, "/").concat(conf)));
-
-          case 23:
-            fetchedConfig = _context.sent;
-            _context.next = 29;
-            break;
-
-          case 26:
-            _context.prev = 26;
-            _context.t0 = _context["catch"](20);
-            console.error("tried to access ".concat(baseConfigLocation, "/").concat(conf, ", but failed"));
-
-          case 29:
-            _newConfig = mergeConfigs(_newConfig, fetchedConfig) || {};
-
-          case 30:
-            _i3++;
-            _context.next = 17;
-            break;
-
-          case 33:
-            if (dataRootReg[protocol]) {
-              _newConfig.dataRoot = dataRootReg[protocol];
-            }
-
-            return _context.abrupt("return", createFinalConfig(_newConfig));
-
-          case 35:
-            newConfig = (0, _jb1ConfigParse.regularizeConf)(baseConfig, window.location.href);
-
-            if (dataRootReg[protocol]) {
-              newConfig.dataRoot = dataRootReg[protocol];
+function fetchJb1(dataRoot, baseConfig, baseConfigRoot) {
+    if (dataRoot === void 0) { dataRoot = { uri: '', locationType: 'UriLocation' }; }
+    if (baseConfig === void 0) { baseConfig = {
+        include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
+    }; }
+    if (baseConfigRoot === void 0) { baseConfigRoot = { uri: '', locationType: 'UriLocation' }; }
+    return __awaiter(this, void 0, void 0, function () {
+        var protocol, dataRootReg, dataRootLocation, baseProtocol, baseConfigLocation, newConfig_1, _a, _b, conf, fetchedConfig, error_1, e_1_1, newConfig;
+        var e_1, _c, _d;
+        return __generator(this, function (_e) {
+            switch (_e.label) {
+                case 0:
+                    protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
+                    dataRootReg = JSON.parse(JSON.stringify(dataRoot));
+                    dataRootLocation = '';
+                    if (isUriLocation(dataRoot)) {
+                        dataRootLocation = dataRoot.uri;
+                    }
+                    if (isLocalPathLocation(dataRoot)) {
+                        dataRootLocation = dataRoot.localPath;
+                    }
+                    if (dataRootLocation.endsWith('/')) {
+                        dataRootReg[protocol] = dataRootLocation.slice(0, dataRootLocation.length - 1);
+                    }
+                    if (!((isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||
+                        (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath))) return [3 /*break*/, 12];
+                    baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath';
+                    baseConfigLocation = '';
+                    if (isUriLocation(baseConfigRoot)) {
+                        baseConfigLocation = baseConfigRoot.uri;
+                    }
+                    if (isLocalPathLocation(baseConfigRoot)) {
+                        baseConfigLocation = baseConfigRoot.localPath;
+                    }
+                    if (baseConfigLocation.endsWith('/')) {
+                        baseConfigLocation = baseConfigLocation.slice(0, baseConfigLocation.length - 1);
+                    }
+                    newConfig_1 = {};
+                    _e.label = 1;
+                case 1:
+                    _e.trys.push([1, 9, 10, 11]);
+                    _a = __values(['jbrowse.conf', 'jbrowse_conf.json']), _b = _a.next();
+                    _e.label = 2;
+                case 2:
+                    if (!!_b.done) return [3 /*break*/, 8];
+                    conf = _b.value;
+                    fetchedConfig = null;
+                    _e.label = 3;
+                case 3:
+                    _e.trys.push([3, 5, , 6]);
+                    return [4 /*yield*/, fetchConfigFile((_d = {},
+                            _d[baseProtocol] = "".concat(baseConfigLocation, "/").concat(conf),
+                            _d))];
+                case 4:
+                    // @ts-ignore
+                    fetchedConfig = _e.sent();
+                    return [3 /*break*/, 6];
+                case 5:
+                    error_1 = _e.sent();
+                    console.error("tried to access ".concat(baseConfigLocation, "/").concat(conf, ", but failed"));
+                    return [3 /*break*/, 6];
+                case 6:
+                    newConfig_1 = mergeConfigs(newConfig_1, fetchedConfig) || {};
+                    _e.label = 7;
+                case 7:
+                    _b = _a.next();
+                    return [3 /*break*/, 2];
+                case 8: return [3 /*break*/, 11];
+                case 9:
+                    e_1_1 = _e.sent();
+                    e_1 = { error: e_1_1 };
+                    return [3 /*break*/, 11];
+                case 10:
+                    try {
+                        if (_b && !_b.done && (_c = _a.return)) _c.call(_a);
+                    }
+                    finally { if (e_1) throw e_1.error; }
+                    return [7 /*endfinally*/];
+                case 11:
+                    if (dataRootReg[protocol]) {
+                        newConfig_1.dataRoot = dataRootReg[protocol];
+                    }
+                    return [2 /*return*/, createFinalConfig(newConfig_1)];
+                case 12:
+                    newConfig = (0, jb1ConfigParse_1.regularizeConf)(baseConfig, window.location.href);
+                    if (dataRootReg[protocol]) {
+                        newConfig.dataRoot = dataRootReg[protocol];
+                    }
+                    return [2 /*return*/, createFinalConfig(newConfig)];
             }
-
-            return _context.abrupt("return", createFinalConfig(newConfig));
-
-          case 38:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee, null, [[20, 26]]);
-  }));
-  return _fetchJb.apply(this, arguments);
-}
-
-function createFinalConfig(_x) {
-  return _createFinalConfig.apply(this, arguments);
-}
-
-function _createFinalConfig() {
-  _createFinalConfig = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(baseConfig) {
-    var defaults,
-        configWithDefaults,
-        finalConfig,
-        _args2 = arguments;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            defaults = _args2.length > 1 && _args2[1] !== undefined ? _args2[1] : configDefaults;
-            configWithDefaults = (0, _util.deepUpdate)((0, _util.clone)(defaults), baseConfig);
-            _context2.next = 4;
-            return loadIncludes(configWithDefaults);
-
-          case 4:
-            finalConfig = _context2.sent;
-            finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig;
-            fillTemplates(finalConfig, finalConfig);
-            validateConfig(finalConfig);
-            return _context2.abrupt("return", finalConfig);
-
-          case 9:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  }));
-  return _createFinalConfig.apply(this, arguments);
-}
-
-function fetchConfigFile(_x2) {
-  return _fetchConfigFile.apply(this, arguments);
+        });
+    });
 }
-
-function _fetchConfigFile() {
-  _fetchConfigFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3(location) {
-    var result;
-    return _regenerator.default.wrap(function _callee3$(_context3) {
-      while (1) {
-        switch (_context3.prev = _context3.next) {
-          case 0:
-            _context3.next = 2;
-            return (0, _io.openLocation)(location).readFile('utf8');
-
-          case 2:
-            result = _context3.sent;
-
-            if (!isUriLocation(location)) {
-              _context3.next = 5;
-              break;
+exports.fetchJb1 = fetchJb1;
+function createFinalConfig(baseConfig, defaults) {
+    if (defaults === void 0) { defaults = configDefaults; }
+    return __awaiter(this, void 0, void 0, function () {
+        var configWithDefaults, finalConfig;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0:
+                    configWithDefaults = (0, util_1.deepUpdate)((0, util_1.clone)(defaults), baseConfig);
+                    return [4 /*yield*/, loadIncludes(configWithDefaults)];
+                case 1:
+                    finalConfig = _a.sent();
+                    finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig;
+                    fillTemplates(finalConfig, finalConfig);
+                    validateConfig(finalConfig);
+                    return [2 /*return*/, finalConfig];
             }
-
-            return _context3.abrupt("return", parseJb1(result, location.uri));
-
-          case 5:
-            if (!isLocalPathLocation(location)) {
-              _context3.next = 7;
-              break;
+        });
+    });
+}
+exports.createFinalConfig = createFinalConfig;
+function fetchConfigFile(location) {
+    return __awaiter(this, void 0, void 0, function () {
+        var result;
+        return __generator(this, function (_a) {
+            switch (_a.label) {
+                case 0: return [4 /*yield*/, (0, io_1.openLocation)(location).readFile('utf8')];
+                case 1:
+                    result = _a.sent();
+                    if (isUriLocation(location)) {
+                        return [2 /*return*/, parseJb1(result, location.uri)];
+                    }
+                    if (isLocalPathLocation(location)) {
+                        return [2 /*return*/, parseJb1(result, location.localPath)];
+                    }
+                    return [2 /*return*/, parseJb1(result)];
             }
-
-            return _context3.abrupt("return", parseJb1(result, location.localPath));
-
-          case 7:
-            return _context3.abrupt("return", parseJb1(result));
-
-          case 8:
-          case "end":
-            return _context3.stop();
-        }
-      }
-    }, _callee3);
-  }));
-  return _fetchConfigFile.apply(this, arguments);
+        });
+    });
 }
-
-function parseJb1(config) {
-  var url = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : '';
-
-  if (config.trim().startsWith('{')) {
-    return (0, _jb1ConfigParse.parseJB1Json)(config, url);
-  }
-
-  return (0, _jb1ConfigParse.parseJB1Conf)(config, url);
+exports.fetchConfigFile = fetchConfigFile;
+function parseJb1(config, url) {
+    if (url === void 0) { url = ''; }
+    if (config.trim().startsWith('{')) {
+        return (0, jb1ConfigParse_1.parseJB1Json)(config, url);
+    }
+    return (0, jb1ConfigParse_1.parseJB1Conf)(config, url);
 }
+exports.parseJb1 = parseJb1;
 /**
  * Merges config object b into a. Properties in b override those in a.
  */
-
-
 function mergeConfigs(a, b) {
-  if (b === null) {
-    return null;
-  }
-
-  if (a === null) {
-    a = {};
-  }
-
-  for (var _i = 0, _Object$keys = Object.keys(b); _i < _Object$keys.length; _i++) {
-    var prop = _Object$keys[_i];
-
-    if (prop === 'tracks' && prop in a) {
-      var aTracks = a[prop] || [];
-      var bTracks = b[prop] || [];
-
-      if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
-        a[prop] = mergeTrackConfigs(aTracks || [], bTracks || []);
-      } else {
-        throw new Error("Track config has not been properly regularized: ".concat(aTracks, " ").concat(bTracks));
-      }
-    } else if (!noRecursiveMerge(prop) && prop in a && // @ts-ignore
-    (0, _typeof2.default)(b[prop]) === 'object' && // @ts-ignore
-    (0, _typeof2.default)(a[prop]) === 'object') {
-      // @ts-ignore
-      a[prop] = (0, _util.deepUpdate)(a[prop], b[prop]);
-    } else if (prop === 'dataRoot') {
-      if (a[prop] === undefined || a[prop] === 'data' && b[prop] !== undefined) {
-        a[prop] = b[prop];
-      } // @ts-ignore
-
-    } else if (a[prop] === undefined || b[prop] !== undefined) {
-      // @ts-ignore
-      a[prop] = b[prop];
+    var e_2, _a;
+    if (b === null) {
+        return null;
     }
-  }
-
-  return a;
+    if (a === null) {
+        a = {};
+    }
+    try {
+        for (var _b = __values(Object.keys(b)), _c = _b.next(); !_c.done; _c = _b.next()) {
+            var prop = _c.value;
+            if (prop === 'tracks' && prop in a) {
+                var aTracks = a[prop] || [];
+                var bTracks = b[prop] || [];
+                if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
+                    a[prop] = mergeTrackConfigs(aTracks || [], bTracks || []);
+                }
+                else {
+                    throw new Error("Track config has not been properly regularized: ".concat(aTracks, " ").concat(bTracks));
+                }
+            }
+            else if (!noRecursiveMerge(prop) &&
+                prop in a &&
+                // @ts-ignore
+                typeof b[prop] === 'object' &&
+                // @ts-ignore
+                typeof a[prop] === 'object') {
+                // @ts-ignore
+                a[prop] = (0, util_1.deepUpdate)(a[prop], b[prop]);
+            }
+            else if (prop === 'dataRoot') {
+                if (a[prop] === undefined ||
+                    (a[prop] === 'data' && b[prop] !== undefined)) {
+                    a[prop] = b[prop];
+                }
+                // @ts-ignore
+            }
+            else if (a[prop] === undefined || b[prop] !== undefined) {
+                // @ts-ignore
+                a[prop] = b[prop];
+            }
+        }
+    }
+    catch (e_2_1) { e_2 = { error: e_2_1 }; }
+    finally {
+        try {
+            if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
+        }
+        finally { if (e_2) throw e_2.error; }
+    }
+    return a;
 }
 /**
  * Special-case merging of two `tracks` configuration arrays.
  */
-
-
 function mergeTrackConfigs(a, b) {
-  if (!b.length) {
-    return a;
-  } // index the tracks in `a` by track label
-
-
-  var aTracks = {};
-  a.forEach(function (t, i) {
-    t.index = i;
-    aTracks[t.label] = t;
-  });
-  b.forEach(function (bT) {
-    var aT = aTracks[bT.label];
-
-    if (aT) {
-      mergeConfigs(aT, bT);
-    } else {
-      a.push(bT);
+    if (!b.length) {
+        return a;
     }
-  });
-  return a;
+    // index the tracks in `a` by track label
+    var aTracks = {};
+    a.forEach(function (t, i) {
+        t.index = i;
+        aTracks[t.label] = t;
+    });
+    b.forEach(function (bT) {
+        var aT = aTracks[bT.label];
+        if (aT) {
+            mergeConfigs(aT, bT);
+        }
+        else {
+            a.push(bT);
+        }
+    });
+    return a;
 }
 /**
  * Recursively fetch, parse, and merge all the includes in the given config
  * object.  Calls the callback with the resulting configuration when finished.
  * @param inputConfig - Config to load includes into
  */
-
-
-function loadIncludes(_x3) {
-  return _loadIncludes.apply(this, arguments);
-}
-
-function _loadIncludes() {
-  _loadIncludes = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(inputConfig) {
-    var loadRecur, _loadRecur;
-
-    return _regenerator.default.wrap(function _callee6$(_context6) {
-      while (1) {
-        switch (_context6.prev = _context6.next) {
-          case 0:
-            _loadRecur = function _loadRecur3() {
-              _loadRecur = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(config, upstreamConf) {
+function loadIncludes(inputConfig) {
+    return __awaiter(this, void 0, void 0, function () {
+        function loadRecur(config, upstreamConf) {
+            return __awaiter(this, void 0, void 0, function () {
                 var sourceUrl, newUpstreamConf, includes, loads, includedDataObjects;
-                return _regenerator.default.wrap(function _callee5$(_context5) {
-                  while (1) {
-                    switch (_context5.prev = _context5.next) {
-                      case 0:
-                        sourceUrl = config.sourceUrl || config.baseUrl;
-
-                        if (sourceUrl) {
-                          _context5.next = 3;
-                          break;
-                        }
-
-                        throw new Error("Could not determine source URL: ".concat(JSON.stringify(config)));
-
-                      case 3:
-                        newUpstreamConf = mergeConfigs((0, _util.clone)(upstreamConf), config);
-
-                        if (newUpstreamConf) {
-                          _context5.next = 6;
-                          break;
-                        }
-
-                        throw new Error('Problem merging configs');
-
-                      case 6:
-                        includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
-                        delete config.include;
-                        loads = includes.map( /*#__PURE__*/function () {
-                          var _ref = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(include) {
-                            var includedData;
-                            return _regenerator.default.wrap(function _callee4$(_context4) {
-                              while (1) {
-                                switch (_context4.prev = _context4.next) {
-                                  case 0:
-                                    include.cacheBuster = inputConfig.cacheBuster;
-                                    _context4.next = 3;
-                                    return fetchConfigFile({
-                                      uri: new URL(include.url, sourceUrl).href,
-                                      locationType: 'UriLocation'
-                                    });
-
-                                  case 3:
-                                    includedData = _context4.sent;
-                                    return _context4.abrupt("return", loadRecur(includedData, newUpstreamConf));
-
-                                  case 5:
-                                  case "end":
-                                    return _context4.stop();
-                                }
-                              }
-                            }, _callee4);
-                          }));
-
-                          return function (_x6) {
-                            return _ref.apply(this, arguments);
-                          };
-                        }());
-                        _context5.next = 11;
-                        return Promise.all(loads);
-
-                      case 11:
-                        includedDataObjects = _context5.sent;
-                        includedDataObjects.forEach(function (includedData) {
-                          config = mergeConfigs(config, includedData) || config;
-                        });
-                        return _context5.abrupt("return", config);
-
-                      case 14:
-                      case "end":
-                        return _context5.stop();
+                var _this = this;
+                return __generator(this, function (_a) {
+                    switch (_a.label) {
+                        case 0:
+                            sourceUrl = config.sourceUrl || config.baseUrl;
+                            if (!sourceUrl) {
+                                throw new Error("Could not determine source URL: ".concat(JSON.stringify(config)));
+                            }
+                            newUpstreamConf = mergeConfigs((0, util_1.clone)(upstreamConf), config);
+                            if (!newUpstreamConf) {
+                                throw new Error('Problem merging configs');
+                            }
+                            includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
+                            delete config.include;
+                            loads = includes.map(function (include) { return __awaiter(_this, void 0, void 0, function () {
+                                var includedData;
+                                return __generator(this, function (_a) {
+                                    switch (_a.label) {
+                                        case 0:
+                                            include.cacheBuster = inputConfig.cacheBuster;
+                                            return [4 /*yield*/, fetchConfigFile({
+                                                    uri: new URL(include.url, sourceUrl).href,
+                                                    locationType: 'UriLocation',
+                                                })];
+                                        case 1:
+                                            includedData = _a.sent();
+                                            return [2 /*return*/, loadRecur(includedData, newUpstreamConf)];
+                                    }
+                                });
+                            }); });
+                            return [4 /*yield*/, Promise.all(loads)];
+                        case 1:
+                            includedDataObjects = _a.sent();
+                            includedDataObjects.forEach(function (includedData) {
+                                config = mergeConfigs(config, includedData) || config;
+                            });
+                            return [2 /*return*/, config];
                     }
-                  }
-                }, _callee5);
-              }));
-              return _loadRecur.apply(this, arguments);
-            };
-
-            loadRecur = function _loadRecur2(_x4, _x5) {
-              return _loadRecur.apply(this, arguments);
-            };
-
-            inputConfig = (0, _util.clone)(inputConfig);
-            return _context6.abrupt("return", loadRecur(inputConfig, {}));
-
-          case 4:
-          case "end":
-            return _context6.stop();
+                });
+            });
         }
-      }
-    }, _callee6);
-  }));
-  return _loadIncludes.apply(this, arguments);
+        return __generator(this, function (_a) {
+            inputConfig = (0, util_1.clone)(inputConfig);
+            return [2 /*return*/, loadRecur(inputConfig, {})];
+        });
+    });
 }
-
 function regularizeIncludes(includes) {
-  if (!includes) {
-    return [];
-  } // coerce include to an array
-
-
-  if (!Array.isArray(includes)) {
-    includes = [includes];
-  }
-
-  return includes.map(function (include) {
-    // coerce bare strings in the includes to URLs
-    if (typeof include === 'string') {
-      include = {
-        url: include
-      };
-    } // set defaults for format and version
-
-
-    if (!('format' in include)) {
-      include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json';
+    if (!includes) {
+        return [];
     }
-
-    if (include.format === 'JB_json' && !('version' in include)) {
-      include.version = 1;
+    // coerce include to an array
+    if (!Array.isArray(includes)) {
+        includes = [includes];
     }
-
-    return include;
-  });
-} // eslint-disable-next-line @typescript-eslint/no-explicit-any,@typescript-eslint/no-unnecessary-type-constraint
-
-
+    return includes.map(function (include) {
+        // coerce bare strings in the includes to URLs
+        if (typeof include === 'string') {
+            include = { url: include };
+        }
+        // set defaults for format and version
+        if (!('format' in include)) {
+            include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json';
+        }
+        if (include.format === 'JB_json' && !('version' in include)) {
+            include.version = 1;
+        }
+        return include;
+    });
+}
+// eslint-disable-next-line @typescript-eslint/no-explicit-any,@typescript-eslint/no-unnecessary-type-constraint
 function fillTemplates(subconfig, config) {
-  if (!subconfig) {
-    return subconfig;
-  }
-
-  if (Array.isArray(subconfig)) {
-    for (var i = 0; i < subconfig.length; i += 1) {
-      subconfig[i] = fillTemplates(subconfig[i], config);
+    var e_3, _a;
+    if (!subconfig) {
+        return subconfig;
     }
-  } else if ((0, _typeof2.default)(subconfig) === 'object') {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    var sub = subconfig;
-
-    for (var _i2 = 0, _Object$keys2 = Object.keys(sub); _i2 < _Object$keys2.length; _i2++) {
-      var name = _Object$keys2[_i2];
-      sub[name] = fillTemplates(sub[name], config);
+    if (Array.isArray(subconfig)) {
+        for (var i = 0; i < subconfig.length; i += 1) {
+            subconfig[i] = fillTemplates(subconfig[i], config);
+        }
     }
-  } else if (typeof subconfig === 'string') {
-    // @ts-ignore
-    return (0, _util.fillTemplate)(subconfig, config);
-  }
-
-  return subconfig;
+    else if (typeof subconfig === 'object') {
+        // eslint-disable-next-line @typescript-eslint/no-explicit-any
+        var sub = subconfig;
+        try {
+            for (var _b = __values(Object.keys(sub)), _c = _b.next(); !_c.done; _c = _b.next()) {
+                var name_1 = _c.value;
+                sub[name_1] = fillTemplates(sub[name_1], config);
+            }
+        }
+        catch (e_3_1) { e_3 = { error: e_3_1 }; }
+        finally {
+            try {
+                if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
+            }
+            finally { if (e_3) throw e_3.error; }
+        }
+    }
+    else if (typeof subconfig === 'string') {
+        // @ts-ignore
+        return (0, util_1.fillTemplate)(subconfig, config);
+    }
+    return subconfig;
 }
 /**
  * list of config properties that should not be recursively merged
  * @param propName - name of config property
  */
-
-
 function noRecursiveMerge(propName) {
-  return propName === 'datasets';
+    return propName === 'datasets';
 }
-
 var configDefaults = {
-  tracks: [],
-  containerID: 'GenomeBrowser',
-  dataRoot: 'data',
-  show_tracklist: true,
-  show_nav: true,
-  show_menu: true,
-  show_overview: true,
-  show_fullviewlink: true,
-  update_browser_title: true,
-  updateBrowserURL: true,
-  refSeqs: '{dataRoot}/seq/refSeqs.json',
-  include: ['jbrowse.conf', 'jbrowse_conf.json'],
-  nameUrl: '{dataRoot}/names/root.json',
-  datasets: {
-    _DEFAULT_EXAMPLES: true,
-    volvox: {
-      url: '?data=sample_data/json/volvox',
-      name: 'Volvox Example'
-    },
-    modencode: {
-      url: '?data=sample_data/json/modencode',
-      name: 'MODEncode Example'
+    tracks: [],
+    containerID: 'GenomeBrowser',
+    dataRoot: 'data',
+    show_tracklist: true,
+    show_nav: true,
+    show_menu: true,
+    show_overview: true,
+    show_fullviewlink: true,
+    update_browser_title: true,
+    updateBrowserURL: true,
+    refSeqs: '{dataRoot}/seq/refSeqs.json',
+    include: ['jbrowse.conf', 'jbrowse_conf.json'],
+    nameUrl: '{dataRoot}/names/root.json',
+    datasets: {
+        _DEFAULT_EXAMPLES: true,
+        volvox: { url: '?data=sample_data/json/volvox', name: 'Volvox Example' },
+        modencode: {
+            url: '?data=sample_data/json/modencode',
+            name: 'MODEncode Example',
+        },
+        yeast: { url: '?data=sample_data/json/yeast', name: 'Yeast Example' },
     },
-    yeast: {
-      url: '?data=sample_data/json/yeast',
-      name: 'Yeast Example'
-    }
-  },
-  highlightSearchedRegions: false,
-  highResolutionMode: 'auto'
+    highlightSearchedRegions: false,
+    highResolutionMode: 'auto',
 };
 /**
  * Examine the loaded and merged configuration for errors.  Throws
  * exceptions if it finds anything amiss.
  * @returns nothing meaningful
  */
-
 function validateConfig(config) {
-  if (!config.tracks) {
-    config.tracks = [];
-  }
-
-  if (!config.baseUrl) {
-    throw new Error('Must provide a `baseUrl` in configuration');
-  }
-}
+    if (!config.tracks) {
+        config.tracks = [];
+    }
+    if (!config.baseUrl) {
+        throw new Error('Must provide a `baseUrl` in configuration');
+    }
+}
+//# sourceMappingURL=jb1ConfigLoad.js.map