@jbrowse/core 2.0.1 → 2.1.0

package/assemblyManager/assembly.js

@@ -1,577 +1,302 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = assemblyFactory;
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _objectWithoutProperties2 = _interopRequireDefault(require("@babel/runtime/helpers/objectWithoutProperties"));
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _jsonStableStringify = _interopRequireDefault(require("json-stable-stringify"));
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
-
-var _configuration = require("../configuration");
-
-var _util = require("../util");
-
-var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
-
-var _excluded = ["signal", "statusCallback"];
-
-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 refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'); // Based on the UCSC Genome Browser chromosome color palette:
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const json_stable_stringify_1 = __importDefault(require("json-stable-stringify"));
+const mobx_state_tree_1 = require("mobx-state-tree");
+const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
+const configuration_1 = require("../configuration");
+const util_1 = require("../util");
+const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
+const refNameRegex = new RegExp('[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*');
+// Based on the UCSC Genome Browser chromosome color palette:
 // https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
 // Some colors darkened to have at least a 3:1 contrast ratio on a white
 // background
-
-var refNameColors = ['rgb(153, 102, 0)', 'rgb(102, 102, 0)', 'rgb(153, 153, 30)', 'rgb(204, 0, 0)', 'rgb(255, 0, 0)', 'rgb(255, 0, 204)', 'rgb(165, 132, 132)', // originally 'rgb(255, 204, 204)'
-'rgb(204, 122, 0)', // originally rgb(255, 153, 0)'
-'rgb(178, 142, 0)', // originally 'rgb(255, 204, 0)'
-'rgb(153, 153, 0)', // originally 'rgb(255, 255, 0)'
-'rgb(122, 153, 0)', // originally 'rgb(204, 255, 0)'
-'rgb(0, 165, 0)', // originally 'rgb(0, 255, 0)'
-'rgb(53, 128, 0)', 'rgb(0, 0, 204)', 'rgb(96, 145, 242)', // originally 'rgb(102, 153, 255)'
-'rgb(107, 142, 178)', // originally 'rgb(153, 204, 255)'
-'rgb(0, 165, 165)', // originally 'rgb(0, 255, 255)'
-'rgb(122, 153, 153)', // originally 'rgb(204, 255, 255)'
-'rgb(153, 0, 204)', 'rgb(204, 51, 255)', 'rgb(173, 130, 216)', // originally 'rgb(204, 153, 255)'
-'rgb(102, 102, 102)', 'rgb(145, 145, 145)', // originally 'rgb(153, 153, 153)'
-'rgb(142, 142, 142)', // originally 'rgb(204, 204, 204)'
-'rgb(142, 142, 107)', // originally 'rgb(204, 204, 153)'
-'rgb(96, 163, 48)' // originally 'rgb(121, 204, 61)'
+const refNameColors = [
+    'rgb(153, 102, 0)',
+    'rgb(102, 102, 0)',
+    'rgb(153, 153, 30)',
+    'rgb(204, 0, 0)',
+    'rgb(255, 0, 0)',
+    'rgb(255, 0, 204)',
+    'rgb(165, 132, 132)',
+    'rgb(204, 122, 0)',
+    'rgb(178, 142, 0)',
+    'rgb(153, 153, 0)',
+    'rgb(122, 153, 0)',
+    'rgb(0, 165, 0)',
+    'rgb(53, 128, 0)',
+    'rgb(0, 0, 204)',
+    'rgb(96, 145, 242)',
+    'rgb(107, 142, 178)',
+    'rgb(0, 165, 165)',
+    'rgb(122, 153, 153)',
+    'rgb(153, 0, 204)',
+    'rgb(204, 51, 255)',
+    'rgb(173, 130, 216)',
+    'rgb(102, 102, 102)',
+    'rgb(145, 145, 145)',
+    'rgb(142, 142, 142)',
+    'rgb(142, 142, 107)',
+    'rgb(96, 163, 48)', // originally 'rgb(121, 204, 61)'
 ];
-
-function loadRefNameMap(_x, _x2, _x3, _x4) {
-  return _loadRefNameMap.apply(this, arguments);
-} // Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
-
-
-function _loadRefNameMap() {
-  _loadRefNameMap = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4(assembly, adapterConfig, options, signal) {
-    var sessionId, refNames, refNameAliases, refNameMap, reversed;
-    return _regenerator.default.wrap(function _callee4$(_context4) {
-      while (1) {
-        switch (_context4.prev = _context4.next) {
-          case 0:
-            sessionId = options.sessionId;
-            _context4.next = 3;
-            return (0, _util.when)(function () {
-              return Boolean(assembly.regions && assembly.refNameAliases);
-            }, {
-              signal: signal,
-              name: 'when assembly ready'
-            });
-
-          case 3:
-            _context4.next = 5;
-            return assembly.rpcManager.call(sessionId, 'CoreGetRefNames', _objectSpread({
-              adapterConfig: adapterConfig,
-              signal: signal
-            }, options), {
-              timeout: 1000000
-            });
-
-          case 5:
-            refNames = _context4.sent;
-            refNameAliases = assembly.refNameAliases;
-
-            if (refNameAliases) {
-              _context4.next = 9;
-              break;
-            }
-
-            throw new Error("error loading assembly ".concat(assembly.name, "'s refNameAliases"));
-
-          case 9:
-            refNameMap = Object.fromEntries(refNames.map(function (name) {
-              checkRefName(name);
-              return [assembly.getCanonicalRefName(name), name];
-            })); // make the reversed map too
-
-            reversed = Object.fromEntries(Object.entries(refNameMap).map(function (_ref2) {
-              var _ref3 = (0, _slicedToArray2.default)(_ref2, 2),
-                  canonicalName = _ref3[0],
-                  adapterName = _ref3[1];
-
-              return [adapterName, canonicalName];
-            }));
-            return _context4.abrupt("return", {
-              forwardMap: refNameMap,
-              reverseMap: reversed
-            });
-
-          case 12:
-          case "end":
-            return _context4.stop();
-        }
-      }
-    }, _callee4);
-  }));
-  return _loadRefNameMap.apply(this, arguments);
+async function loadRefNameMap(assembly, adapterConfig, options, signal) {
+    const { sessionId } = options;
+    await (0, util_1.when)(() => Boolean(assembly.regions && assembly.refNameAliases), {
+        signal,
+        name: 'when assembly ready',
+    });
+    const refNames = (await assembly.rpcManager.call(sessionId, 'CoreGetRefNames', {
+        adapterConfig,
+        signal,
+        ...options,
+    }, { timeout: 1000000 }));
+    const { refNameAliases } = assembly;
+    if (!refNameAliases) {
+        throw new Error(`error loading assembly ${assembly.name}'s refNameAliases`);
+    }
+    const refNameMap = Object.fromEntries(refNames.map(name => {
+        checkRefName(name);
+        return [assembly.getCanonicalRefName(name), name];
+    }));
+    // make the reversed map too
+    const reversed = Object.fromEntries(Object.entries(refNameMap).map(([canonicalName, adapterName]) => [
+        adapterName,
+        canonicalName,
+    ]));
+    return {
+        forwardMap: refNameMap,
+        reverseMap: reversed,
+    };
 }
-
+// Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
 function checkRefName(refName) {
-  if (!refName.match(refNameRegex)) {
-    throw new Error("Encountered invalid refName: \"".concat(refName, "\""));
-  }
+    if (!refName.match(refNameRegex)) {
+        throw new Error(`Encountered invalid refName: "${refName}"`);
+    }
 }
-
 function getAdapterId(adapterConf) {
-  return (0, _jsonStableStringify.default)(adapterConf);
+    return (0, json_stable_stringify_1.default)(adapterConf);
 }
-
 function assemblyFactory(assemblyConfigType, pluginManager) {
-  var adapterLoads = new _abortablePromiseCache.default({
-    cache: new _QuickLRU.default({
-      maxSize: 1000
-    }),
-    fill: function fill(args, abortSignal, statusCallback) {
-      return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var adapterConf, self, options;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                adapterConf = args.adapterConf, self = args.self, options = args.options;
-                return _context.abrupt("return", loadRefNameMap(self, adapterConf, _objectSpread(_objectSpread({}, options), {}, {
-                  statusCallback: statusCallback
-                }), abortSignal));
-
-              case 2:
-              case "end":
-                return _context.stop();
+    const adapterLoads = new abortable_promise_cache_1.default({
+        cache: new QuickLRU_1.default({ maxSize: 1000 }),
+        async fill(args, abortSignal, statusCallback) {
+            const { adapterConf, self, options } = args;
+            return loadRefNameMap(self, adapterConf, { ...options, statusCallback }, abortSignal);
+        },
+    });
+    return mobx_state_tree_1.types
+        .model({
+        configuration: mobx_state_tree_1.types.safeReference(assemblyConfigType),
+    })
+        .volatile(() => ({
+        error: undefined,
+        regions: undefined,
+        refNameAliases: undefined,
+        lowerCaseRefNameAliases: undefined,
+        cytobands: undefined,
+    }))
+        .views(self => ({
+        get initialized() {
+            return !!self.refNameAliases;
+        },
+        get name() {
+            return (0, configuration_1.getConf)(self, 'name');
+        },
+        get aliases() {
+            return (0, configuration_1.getConf)(self, 'aliases');
+        },
+        hasName(name) {
+            return this.allAliases.includes(name);
+        },
+        get allAliases() {
+            return [this.name, ...this.aliases];
+        },
+        get refNames() {
+            var _a;
+            return (_a = self.regions) === null || _a === void 0 ? void 0 : _a.map(region => region.refName);
+        },
+        // note: lowerCaseRefNameAliases not included here: this allows the list
+        // of refnames to be just the "normal casing", but things like
+        // getCanonicalRefName can resolve a lower-case name if needed
+        get allRefNames() {
+            return !self.refNameAliases
+                ? undefined
+                : Object.keys(self.refNameAliases);
+        },
+        get rpcManager() {
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            return (0, mobx_state_tree_1.getParent)(self, 2).rpcManager;
+        },
+        get refNameColors() {
+            const colors = (0, configuration_1.getConf)(self, 'refNameColors');
+            return colors.length === 0 ? refNameColors : colors;
+        },
+    }))
+        .views(self => ({
+        getCanonicalRefName(refName) {
+            if (!self.refNameAliases || !self.lowerCaseRefNameAliases) {
+                throw new Error('aliases not loaded, we expect them to be loaded before getCanonicalRefName can be called');
             }
-          }
-        }, _callee);
-      }))();
-    }
-  });
-  return _mobxStateTree.types.model({
-    configuration: _mobxStateTree.types.safeReference(assemblyConfigType)
-  }).volatile(function () {
-    return {
-      error: undefined,
-      regions: undefined,
-      refNameAliases: undefined,
-      lowerCaseRefNameAliases: undefined,
-      cytobands: undefined
-    };
-  }).views(function (self) {
-    return {
-      get initialized() {
-        return !!self.refNameAliases;
-      },
-
-      get name() {
-        return (0, _configuration.getConf)(self, 'name');
-      },
-
-      get aliases() {
-        return (0, _configuration.getConf)(self, 'aliases');
-      },
-
-      hasName: function hasName(name) {
-        return this.allAliases.includes(name);
-      },
-
-      get allAliases() {
-        return [this.name].concat((0, _toConsumableArray2.default)(this.aliases));
-      },
-
-      get refNames() {
-        var _self$regions;
-
-        return (_self$regions = self.regions) === null || _self$regions === void 0 ? void 0 : _self$regions.map(function (region) {
-          return region.refName;
-        });
-      },
-
-      // note: lowerCaseRefNameAliases not included here: this allows the list
-      // of refnames to be just the "normal casing", but things like
-      // getCanonicalRefName can resolve a lower-case name if needed
-      get allRefNames() {
-        return !self.refNameAliases ? undefined : Object.keys(self.refNameAliases);
-      },
-
-      get rpcManager() {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        return (0, _mobxStateTree.getParent)(self, 2).rpcManager;
-      },
-
-      get refNameColors() {
-        var colors = (0, _configuration.getConf)(self, 'refNameColors');
-        return colors.length === 0 ? refNameColors : colors;
-      }
-
-    };
-  }).views(function (self) {
-    return {
-      getCanonicalRefName: function getCanonicalRefName(refName) {
-        if (!self.refNameAliases || !self.lowerCaseRefNameAliases) {
-          throw new Error('aliases not loaded, we expect them to be loaded before getCanonicalRefName can be called');
-        }
-
-        return self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName];
-      },
-      getRefNameColor: function getRefNameColor(refName) {
-        var _self$refNames;
-
-        var idx = (_self$refNames = self.refNames) === null || _self$refNames === void 0 ? void 0 : _self$refNames.findIndex(function (r) {
-          return r === refName;
-        });
-
-        if (idx === undefined || idx === -1) {
-          return undefined;
-        }
-
-        return self.refNameColors[idx % self.refNameColors.length];
-      },
-      isValidRefName: function isValidRefName(refName) {
-        if (!self.refNameAliases) {
-          throw new Error('isValidRefName cannot be called yet, the assembly has not finished loading');
-        }
-
-        return !!this.getCanonicalRefName(refName);
-      }
-    };
-  }).actions(function (self) {
-    return {
-      setLoading: function setLoading() {},
-      setLoaded: function setLoaded(_ref) {
-        var adapterRegionsWithAssembly = _ref.adapterRegionsWithAssembly,
-            refNameAliases = _ref.refNameAliases,
-            lowerCaseRefNameAliases = _ref.lowerCaseRefNameAliases,
-            cytobands = _ref.cytobands;
-        this.setRegions(adapterRegionsWithAssembly);
-        this.setRefNameAliases(refNameAliases, lowerCaseRefNameAliases);
-        this.setCytobands(cytobands);
-      },
-      setError: function setError(e) {
-        console.error(e);
-        self.error = e;
-      },
-      setRegions: function setRegions(regions) {
-        self.regions = regions;
-      },
-      setRefNameAliases: function setRefNameAliases(refNameAliases, lowerCaseRefNameAliases) {
-        self.refNameAliases = refNameAliases;
-        self.lowerCaseRefNameAliases = lowerCaseRefNameAliases;
-      },
-      setCytobands: function setCytobands(cytobands) {
-        self.cytobands = cytobands;
-      },
-      afterAttach: function afterAttach() {
-        (0, _util.makeAbortableReaction)( // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        self, // @ts-ignore
-        makeLoadAssemblyData(pluginManager), loadAssemblyReaction, {
-          name: "".concat(self.name, " assembly loading"),
-          fireImmediately: true
-        }, this.setLoading, this.setLoaded, this.setError);
-      }
-    };
-  }).views(function (self) {
-    return {
-      getAdapterMapEntry: function getAdapterMapEntry(adapterConf, options) {
-        var signal = options.signal,
-            statusCallback = options.statusCallback,
-            rest = (0, _objectWithoutProperties2.default)(options, _excluded);
-
-        if (!options.sessionId) {
-          throw new Error('sessionId is required');
-        }
-
-        var adapterId = getAdapterId(adapterConf);
-        return adapterLoads.get(adapterId, {
-          adapterConf: adapterConf,
-          self: self,
-          options: rest
-        }, // signal intentionally not passed here, fixes issues like #2221.
-        // alternative fix #2540 was proposed but non-working currently
-        undefined, statusCallback);
-      },
-
-      /**
-       * get Map of `canonical-name -> adapter-specific-name`
-       */
-      getRefNameMapForAdapter: function getRefNameMapForAdapter(adapterConf, opts) {
-        var _this = this;
-
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-          var map;
-          return _regenerator.default.wrap(function _callee2$(_context2) {
-            while (1) {
-              switch (_context2.prev = _context2.next) {
-                case 0:
-                  if (!(!opts || !opts.sessionId)) {
-                    _context2.next = 2;
-                    break;
-                  }
-
-                  throw new Error('sessionId is required');
-
-                case 2:
-                  _context2.next = 4;
-                  return _this.getAdapterMapEntry(adapterConf, opts);
-
-                case 4:
-                  map = _context2.sent;
-                  return _context2.abrupt("return", map.forwardMap);
-
-                case 6:
-                case "end":
-                  return _context2.stop();
-              }
+            return (self.refNameAliases[refName] || self.lowerCaseRefNameAliases[refName]);
+        },
+        getRefNameColor(refName) {
+            var _a;
+            const idx = (_a = self.refNames) === null || _a === void 0 ? void 0 : _a.findIndex(r => r === refName);
+            if (idx === undefined || idx === -1) {
+                return undefined;
             }
-          }, _callee2);
-        }))();
-      },
-
-      /**
-       * get Map of `adapter-specific-name -> canonical-name`
-       */
-      getReverseRefNameMapForAdapter: function getReverseRefNameMapForAdapter(adapterConf, opts) {
-        var _this2 = this;
-
-        return (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-          var map;
-          return _regenerator.default.wrap(function _callee3$(_context3) {
-            while (1) {
-              switch (_context3.prev = _context3.next) {
-                case 0:
-                  _context3.next = 2;
-                  return _this2.getAdapterMapEntry(adapterConf, opts);
-
-                case 2:
-                  map = _context3.sent;
-                  return _context3.abrupt("return", map.reverseMap);
-
-                case 4:
-                case "end":
-                  return _context3.stop();
-              }
+            return self.refNameColors[idx % self.refNameColors.length];
+        },
+        isValidRefName(refName) {
+            if (!self.refNameAliases) {
+                throw new Error('isValidRefName cannot be called yet, the assembly has not finished loading');
             }
-          }, _callee3);
-        }))();
-      }
-    };
-  });
+            return !!this.getCanonicalRefName(refName);
+        },
+    }))
+        .actions(self => ({
+        setLoading() { },
+        setLoaded({ adapterRegionsWithAssembly, refNameAliases, lowerCaseRefNameAliases, cytobands, }) {
+            this.setRegions(adapterRegionsWithAssembly);
+            this.setRefNameAliases(refNameAliases, lowerCaseRefNameAliases);
+            this.setCytobands(cytobands);
+        },
+        setError(e) {
+            console.error(e);
+            self.error = e;
+        },
+        setRegions(regions) {
+            self.regions = regions;
+        },
+        setRefNameAliases(refNameAliases, lowerCaseRefNameAliases) {
+            self.refNameAliases = refNameAliases;
+            self.lowerCaseRefNameAliases = lowerCaseRefNameAliases;
+        },
+        setCytobands(cytobands) {
+            self.cytobands = cytobands;
+        },
+        afterAttach() {
+            (0, util_1.makeAbortableReaction)(
+            // eslint-disable-next-line @typescript-eslint/no-explicit-any
+            self, 
+            // @ts-ignore
+            makeLoadAssemblyData(pluginManager), loadAssemblyReaction, { name: `${self.name} assembly loading`, fireImmediately: true }, this.setLoading, this.setLoaded, this.setError);
+        },
+    }))
+        .views(self => ({
+        getAdapterMapEntry(adapterConf, options) {
+            const { signal, statusCallback, ...rest } = options;
+            if (!options.sessionId) {
+                throw new Error('sessionId is required');
+            }
+            const adapterId = getAdapterId(adapterConf);
+            return adapterLoads.get(adapterId, {
+                adapterConf,
+                self: self,
+                options: rest,
+            }, 
+            // signal intentionally not passed here, fixes issues like #2221.
+            // alternative fix #2540 was proposed but non-working currently
+            undefined, statusCallback);
+        },
+        /**
+         * get Map of `canonical-name -> adapter-specific-name`
+         */
+        async getRefNameMapForAdapter(adapterConf, opts) {
+            if (!opts || !opts.sessionId) {
+                throw new Error('sessionId is required');
+            }
+            const map = await this.getAdapterMapEntry(adapterConf, opts);
+            return map.forwardMap;
+        },
+        /**
+         * get Map of `adapter-specific-name -> canonical-name`
+         */
+        async getReverseRefNameMapForAdapter(adapterConf, opts) {
+            const map = await this.getAdapterMapEntry(adapterConf, opts);
+            return map.reverseMap;
+        },
+    }));
 }
-
+exports.default = assemblyFactory;
 function makeLoadAssemblyData(pluginManager) {
-  return function (self) {
-    if (self.configuration) {
-      // use full configuration instead of snapshot of the config, the
-      // rpcManager normally receives a snapshot but we bypass rpcManager here
-      // to avoid spinning up a webworker
-      var _self$configuration = self.configuration,
-          sequence = _self$configuration.sequence,
-          refNameAliases = _self$configuration.refNameAliases,
-          cytobands = _self$configuration.cytobands;
-      var sequenceAdapterConfig = sequence.adapter;
-      var refNameAliasesAdapterConfig = refNameAliases === null || refNameAliases === void 0 ? void 0 : refNameAliases.adapter;
-      var cytobandAdapterConfig = cytobands === null || cytobands === void 0 ? void 0 : cytobands.adapter;
-      return {
-        sequenceAdapterConfig: sequenceAdapterConfig,
-        assemblyName: self.name,
-        refNameAliasesAdapterConfig: refNameAliasesAdapterConfig,
-        cytobandAdapterConfig: cytobandAdapterConfig,
-        pluginManager: pluginManager
-      };
-    }
-
-    return undefined;
-  };
-}
-
-function loadAssemblyReaction(_x5, _x6) {
-  return _loadAssemblyReaction.apply(this, arguments);
-}
-
-function _loadAssemblyReaction() {
-  _loadAssemblyReaction = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(props, signal) {
-    var sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, adapterRegions, adapterRegionsWithAssembly, refNameAliases, aliases, cytobands, lowerCaseRefNameAliases;
-    return _regenerator.default.wrap(function _callee5$(_context5) {
-      while (1) {
-        switch (_context5.prev = _context5.next) {
-          case 0:
-            if (props) {
-              _context5.next = 2;
-              break;
-            }
-
-            return _context5.abrupt("return");
-
-          case 2:
-            sequenceAdapterConfig = props.sequenceAdapterConfig, assemblyName = props.assemblyName, refNameAliasesAdapterConfig = props.refNameAliasesAdapterConfig, cytobandAdapterConfig = props.cytobandAdapterConfig, pluginManager = props.pluginManager;
-            _context5.next = 5;
-            return getAssemblyRegions(sequenceAdapterConfig, pluginManager, signal);
-
-          case 5:
-            adapterRegions = _context5.sent;
-            adapterRegionsWithAssembly = adapterRegions.map(function (adapterRegion) {
-              checkRefName(adapterRegion.refName);
-              return _objectSpread(_objectSpread({}, adapterRegion), {}, {
-                assemblyName: assemblyName
-              });
-            });
-            refNameAliases = {};
-            _context5.next = 10;
-            return getRefNameAliases(refNameAliasesAdapterConfig, pluginManager, signal);
-
-          case 10:
-            aliases = _context5.sent;
-            _context5.next = 13;
-            return getCytobands(cytobandAdapterConfig, pluginManager);
-
-          case 13:
-            cytobands = _context5.sent;
-            aliases.forEach(function (_ref4) {
-              var refName = _ref4.refName,
-                  aliases = _ref4.aliases;
-              aliases.forEach(function (alias) {
-                checkRefName(alias);
-                refNameAliases[alias] = refName;
-              });
-            }); // add identity to the refNameAliases list
-
-            adapterRegionsWithAssembly.forEach(function (region) {
-              refNameAliases[region.refName] = region.refName;
-            });
-            lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(function (_ref5) {
-              var _ref6 = (0, _slicedToArray2.default)(_ref5, 2),
-                  key = _ref6[0],
-                  val = _ref6[1];
-
-              return [key.toLowerCase(), val];
-            }));
-            return _context5.abrupt("return", {
-              adapterRegionsWithAssembly: adapterRegionsWithAssembly,
-              refNameAliases: refNameAliases,
-              lowerCaseRefNameAliases: lowerCaseRefNameAliases,
-              cytobands: cytobands
-            });
-
-          case 18:
-          case "end":
-            return _context5.stop();
+    return (self) => {
+        if (self.configuration) {
+            // use full configuration instead of snapshot of the config, the
+            // rpcManager normally receives a snapshot but we bypass rpcManager here
+            // to avoid spinning up a webworker
+            const { sequence, refNameAliases, cytobands } = self.configuration;
+            const sequenceAdapterConfig = sequence.adapter;
+            const refNameAliasesAdapterConfig = refNameAliases === null || refNameAliases === void 0 ? void 0 : refNameAliases.adapter;
+            const cytobandAdapterConfig = cytobands === null || cytobands === void 0 ? void 0 : cytobands.adapter;
+            return {
+                sequenceAdapterConfig,
+                assemblyName: self.name,
+                refNameAliasesAdapterConfig,
+                cytobandAdapterConfig,
+                pluginManager,
+            };
         }
-      }
-    }, _callee5);
-  }));
-  return _loadAssemblyReaction.apply(this, arguments);
-}
-
-function getRefNameAliases(_x7, _x8, _x9) {
-  return _getRefNameAliases.apply(this, arguments);
+        return undefined;
+    };
 }
-
-function _getRefNameAliases() {
-  _getRefNameAliases = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(config, pluginManager, signal) {
-    var _type$getAdapterClass;
-
-    var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee6$(_context6) {
-      while (1) {
-        switch (_context6.prev = _context6.next) {
-          case 0:
-            type = pluginManager.getAdapterType(config.type);
-            _context6.next = 3;
-            return (_type$getAdapterClass = type.getAdapterClass) === null || _type$getAdapterClass === void 0 ? void 0 : _type$getAdapterClass.call(type);
-
-          case 3:
-            CLASS = _context6.sent;
-            adapter = new CLASS(config, undefined, pluginManager);
-            return _context6.abrupt("return", adapter.getRefNameAliases({
-              signal: signal
-            }));
-
-          case 6:
-          case "end":
-            return _context6.stop();
-        }
-      }
-    }, _callee6);
-  }));
-  return _getRefNameAliases.apply(this, arguments);
+async function loadAssemblyReaction(props, signal) {
+    if (!props) {
+        return;
+    }
+    const { sequenceAdapterConfig, assemblyName, refNameAliasesAdapterConfig, cytobandAdapterConfig, pluginManager, } = props;
+    const adapterRegions = await getAssemblyRegions(sequenceAdapterConfig, pluginManager, signal);
+    const adapterRegionsWithAssembly = adapterRegions.map(adapterRegion => {
+        checkRefName(adapterRegion.refName);
+        return { ...adapterRegion, assemblyName };
+    });
+    const refNameAliases = {};
+    const aliases = await getRefNameAliases(refNameAliasesAdapterConfig, pluginManager, signal);
+    const cytobands = await getCytobands(cytobandAdapterConfig, pluginManager);
+    aliases.forEach(({ refName, aliases }) => {
+        aliases.forEach(alias => {
+            checkRefName(alias);
+            refNameAliases[alias] = refName;
+        });
+    });
+    // add identity to the refNameAliases list
+    adapterRegionsWithAssembly.forEach(region => {
+        refNameAliases[region.refName] = region.refName;
+    });
+    const lowerCaseRefNameAliases = Object.fromEntries(Object.entries(refNameAliases).map(([key, val]) => [
+        key.toLowerCase(),
+        val,
+    ]));
+    return {
+        adapterRegionsWithAssembly,
+        refNameAliases,
+        lowerCaseRefNameAliases,
+        cytobands,
+    };
 }
-
-function getCytobands(_x10, _x11) {
-  return _getCytobands.apply(this, arguments);
+async function getRefNameAliases(config, pluginManager, signal) {
+    var _a;
+    const type = pluginManager.getAdapterType(config.type);
+    const CLASS = await ((_a = type.getAdapterClass) === null || _a === void 0 ? void 0 : _a.call(type));
+    const adapter = new CLASS(config, undefined, pluginManager);
+    return adapter.getRefNameAliases({
+        signal,
+    });
 }
-
-function _getCytobands() {
-  _getCytobands = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(config, pluginManager) {
-    var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee7$(_context7) {
-      while (1) {
-        switch (_context7.prev = _context7.next) {
-          case 0:
-            type = pluginManager.getAdapterType(config.type);
-            _context7.next = 3;
-            return type.getAdapterClass();
-
-          case 3:
-            CLASS = _context7.sent;
-            adapter = new CLASS(config, undefined, pluginManager); // @ts-ignore
-
-            return _context7.abrupt("return", adapter.getData());
-
-          case 6:
-          case "end":
-            return _context7.stop();
-        }
-      }
-    }, _callee7);
-  }));
-  return _getCytobands.apply(this, arguments);
+async function getCytobands(config, pluginManager) {
+    const type = pluginManager.getAdapterType(config.type);
+    const CLASS = await type.getAdapterClass();
+    const adapter = new CLASS(config, undefined, pluginManager);
+    // @ts-ignore
+    return adapter.getData();
 }
-
-function getAssemblyRegions(_x12, _x13, _x14) {
-  return _getAssemblyRegions.apply(this, arguments);
+async function getAssemblyRegions(config, pluginManager, signal) {
+    const type = pluginManager.getAdapterType(config.type);
+    const CLASS = await type.getAdapterClass();
+    const adapter = new CLASS(config, undefined, pluginManager);
+    return adapter.getRegions({ signal });
 }
-
-function _getAssemblyRegions() {
-  _getAssemblyRegions = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(config, pluginManager, signal) {
-    var type, CLASS, adapter;
-    return _regenerator.default.wrap(function _callee8$(_context8) {
-      while (1) {
-        switch (_context8.prev = _context8.next) {
-          case 0:
-            type = pluginManager.getAdapterType(config.type);
-            _context8.next = 3;
-            return type.getAdapterClass();
-
-          case 3:
-            CLASS = _context8.sent;
-            adapter = new CLASS(config, undefined, pluginManager);
-            return _context8.abrupt("return", adapter.getRegions({
-              signal: signal
-            }));
-
-          case 6:
-          case "end":
-            return _context8.stop();
-        }
-      }
-    }, _callee8);
-  }));
-  return _getAssemblyRegions.apply(this, arguments);
-}