@jbrowse/core 2.0.0 → 2.1.2

package/TextSearch/BaseResults.js

@@ -1,126 +1,54 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = exports.RefSequenceResult = void 0;
-
-var _assertThisInitialized2 = _interopRequireDefault(require("@babel/runtime/helpers/assertThisInitialized"));
-
-var _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-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; } }
-
-var BaseResult = /*#__PURE__*/function () {
-  function BaseResult(args) {
-    (0, _classCallCheck2.default)(this, BaseResult);
-    (0, _defineProperty2.default)(this, "label", void 0);
-    (0, _defineProperty2.default)(this, "renderingComponent", void 0);
-    (0, _defineProperty2.default)(this, "displayString", void 0);
-    (0, _defineProperty2.default)(this, "matchedAttribute", void 0);
-    (0, _defineProperty2.default)(this, "matchedObject", void 0);
-    (0, _defineProperty2.default)(this, "textSearchAdapter", void 0);
-    (0, _defineProperty2.default)(this, "relevance", void 0);
-    (0, _defineProperty2.default)(this, "trackId", void 0);
-    (0, _defineProperty2.default)(this, "score", void 0);
-    (0, _defineProperty2.default)(this, "locString", void 0);
-    this.label = args.label;
-    this.locString = args.locString;
-    this.renderingComponent = args.renderingComponent;
-    this.displayString = args.displayString;
-    this.matchedAttribute = args.matchedAttribute;
-    this.matchedObject = args.matchedObject;
-    this.textSearchAdapter = args.textSearchAdapter;
-    this.relevance = args.relevance;
-    this.trackId = args.trackId;
-    this.score = args.score || 1;
-  }
-
-  (0, _createClass2.default)(BaseResult, [{
-    key: "getLabel",
-    value: function getLabel() {
-      return this.label;
-    }
-  }, {
-    key: "getDisplayString",
-    value: function getDisplayString() {
-      return this.displayString || this.label;
-    }
-  }, {
-    key: "getRenderingComponent",
-    value: function getRenderingComponent() {
-      return this.renderingComponent;
-    }
-  }, {
-    key: "getTrackId",
-    value: function getTrackId() {
-      return this.trackId;
-    }
-  }, {
-    key: "getScore",
-    value: function getScore() {
-      return this.score;
-    }
-  }, {
-    key: "updateScore",
-    value: function updateScore(newScore) {
-      this.score = newScore;
-      return this.score;
-    }
-  }, {
-    key: "getId",
-    value: function getId() {
-      return "".concat(this.getLabel(), "-").concat(this.getLocation(), "-").concat(this.getTrackId());
-    }
-  }, {
-    key: "getLocation",
-    value: function getLocation() {
-      return this.locString || this.label;
-    }
-  }]);
-  return BaseResult;
-}();
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.RefSequenceResult = void 0;
+class BaseResult {
+    constructor(args) {
+        this.label = args.label;
+        this.locString = args.locString;
+        this.renderingComponent = args.renderingComponent;
+        this.displayString = args.displayString;
+        this.matchedAttribute = args.matchedAttribute;
+        this.matchedObject = args.matchedObject;
+        this.textSearchAdapter = args.textSearchAdapter;
+        this.relevance = args.relevance;
+        this.trackId = args.trackId;
+        this.score = args.score || 1;
+    }
+    getLabel() {
+        return this.label;
+    }
+    getDisplayString() {
+        return this.displayString || this.label;
+    }
+    getRenderingComponent() {
+        return this.renderingComponent;
+    }
+    getTrackId() {
+        return this.trackId;
+    }
+    getScore() {
+        return this.score;
+    }
+    updateScore(newScore) {
+        this.score = newScore;
+        return this.score;
+    }
+    getId() {
+        return `${this.getLabel()}-${this.getLocation()}-${this.getTrackId()}`;
+    }
+    getLocation() {
+        return this.locString || this.label;
+    }
+}
 exports.default = BaseResult;
-
-var RefSequenceResult = /*#__PURE__*/function (_BaseResult) {
-  (0, _inherits2.default)(RefSequenceResult, _BaseResult);
-
-  var _super = _createSuper(RefSequenceResult);
-
-  function RefSequenceResult(args) {
-    var _args$refName;
-
-    var _this;
-
-    (0, _classCallCheck2.default)(this, RefSequenceResult);
-    _this = _super.call(this, args);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "refName", void 0);
-    _this.refName = (_args$refName = args.refName) !== null && _args$refName !== void 0 ? _args$refName : '';
-    return _this;
-  }
-
-  (0, _createClass2.default)(RefSequenceResult, [{
-    key: "getLocation",
-    value: function getLocation() {
-      return this.refName;
+class RefSequenceResult extends BaseResult {
+    constructor(args) {
+        var _a;
+        super(args);
+        this.refName = (_a = args.refName) !== null && _a !== void 0 ? _a : '';
+    }
+    getLocation() {
+        return this.refName;
     }
-  }]);
-  return RefSequenceResult;
-}(BaseResult);
-
-exports.RefSequenceResult = RefSequenceResult;
+}
+exports.RefSequenceResult = RefSequenceResult;

package/TextSearch/TextSearchManager.js

@@ -1,165 +1,87 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _QuickLRU = _interopRequireDefault(require("../util/QuickLRU"));
-
-var _configuration = require("../configuration");
-
-/*  text-searching controller */
-var TextSearchManager = /*#__PURE__*/function () {
-  function TextSearchManager(pluginManager) {
-    (0, _classCallCheck2.default)(this, TextSearchManager);
-    this.pluginManager = pluginManager;
-    (0, _defineProperty2.default)(this, "adapterCache", void 0);
-    this.adapterCache = new _QuickLRU.default({
-      maxSize: 15
-    });
-  }
-  /**
-   * Instantiate/initialize list of relevant adapters
-   */
-
-
-  (0, _createClass2.default)(TextSearchManager, [{
-    key: "loadTextSearchAdapters",
-    value: function loadTextSearchAdapters(searchScope) {
-      var _this = this;
-
-      return this.relevantAdapters(searchScope).map(function (adapterConfig) {
-        var adapterId = (0, _configuration.readConfObject)(adapterConfig, 'textSearchAdapterId');
-
-        if (_this.adapterCache.has(adapterId)) {
-          return _this.adapterCache.get(adapterId);
-        } else {
-          var _this$pluginManager$g = _this.pluginManager.getTextSearchAdapterType(adapterConfig.type),
-              AdapterClass = _this$pluginManager$g.AdapterClass;
-
-          var adapter = new AdapterClass(adapterConfig, undefined, _this.pluginManager);
-
-          _this.adapterCache.set(adapterId, adapter);
-
-          return adapter;
-        }
-      });
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const QuickLRU_1 = __importDefault(require("../util/QuickLRU"));
+const configuration_1 = require("../configuration");
+class TextSearchManager {
+    constructor(pluginManager) {
+        this.pluginManager = pluginManager;
+        this.adapterCache = new QuickLRU_1.default({
+            maxSize: 15,
+        });
+    }
+    /**
+     * Instantiate/initialize list of relevant adapters
+     */
+    loadTextSearchAdapters(searchScope) {
+        return this.relevantAdapters(searchScope).map(adapterConfig => {
+            const adapterId = (0, configuration_1.readConfObject)(adapterConfig, 'textSearchAdapterId');
+            if (this.adapterCache.has(adapterId)) {
+                return this.adapterCache.get(adapterId);
+            }
+            else {
+                const { AdapterClass } = this.pluginManager.getTextSearchAdapterType(adapterConfig.type);
+                const adapter = new AdapterClass(adapterConfig, undefined, this.pluginManager);
+                this.adapterCache.set(adapterId, adapter);
+                return adapter;
+            }
+        });
     }
     /**
      * Returns list of relevant text search adapters to use
      * @param args - search options/arguments include: search query
      */
-
-  }, {
-    key: "relevantAdapters",
-    value: function relevantAdapters(searchScope) {
-      var _this$pluginManager$r;
-
-      var _ref = (_this$pluginManager$r = this.pluginManager.rootModel) === null || _this$pluginManager$r === void 0 ? void 0 : _this$pluginManager$r.jbrowse,
-          aggregateTextSearchAdapters = _ref.aggregateTextSearchAdapters,
-          tracks = _ref.tracks;
-
-      var assemblyName = searchScope.assemblyName;
-      var relevant = [].concat((0, _toConsumableArray2.default)(this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters)), (0, _toConsumableArray2.default)(this.getTrackAdaptersWithAssembly(assemblyName, tracks)));
-      return relevant;
+    relevantAdapters(searchScope) {
+        var _a;
+        const { aggregateTextSearchAdapters, tracks } = (_a = this.pluginManager.rootModel) === null || _a === void 0 ? void 0 : _a.jbrowse;
+        const { assemblyName } = searchScope;
+        const relevant = [
+            ...this.getAdaptersWithAssembly(assemblyName, aggregateTextSearchAdapters),
+            ...this.getTrackAdaptersWithAssembly(assemblyName, tracks),
+        ];
+        return relevant;
     }
-  }, {
-    key: "getAdaptersWithAssembly",
-    value: function getAdaptersWithAssembly(asmName, adapterConfs) {
-      return adapterConfs.filter(function (conf) {
-        var _readConfObject;
-
-        return (_readConfObject = (0, _configuration.readConfObject)(conf, 'assemblyNames')) === null || _readConfObject === void 0 ? void 0 : _readConfObject.includes(asmName);
-      });
+    getAdaptersWithAssembly(asmName, adapterConfs) {
+        return adapterConfs.filter(conf => { var _a; return (_a = (0, configuration_1.readConfObject)(conf, 'assemblyNames')) === null || _a === void 0 ? void 0 : _a.includes(asmName); });
     }
-  }, {
-    key: "getTrackAdaptersWithAssembly",
-    value: function getTrackAdaptersWithAssembly(asmName, adapterConfs) {
-      var tracksConfs = adapterConfs.filter(function (conf) {
-        var _readConfObject2;
-
-        return (_readConfObject2 = (0, _configuration.readConfObject)(conf, ['textSearching', 'textSearchAdapter', 'assemblyNames'])) === null || _readConfObject2 === void 0 ? void 0 : _readConfObject2.includes(asmName);
-      });
-      var trackAdapters = tracksConfs.map(function (trackConf) {
-        var textSearching = trackConf.textSearching;
-        var textSearchAdapter = textSearching.textSearchAdapter;
-        return textSearchAdapter;
-      });
-      return trackAdapters;
+    getTrackAdaptersWithAssembly(asmName, adapterConfs) {
+        const tracksConfs = adapterConfs.filter(conf => {
+            var _a;
+            return (_a = (0, configuration_1.readConfObject)(conf, [
+                'textSearching',
+                'textSearchAdapter',
+                'assemblyNames',
+            ])) === null || _a === void 0 ? void 0 : _a.includes(asmName);
+        });
+        const trackAdapters = tracksConfs.map(trackConf => {
+            const { textSearching } = trackConf;
+            const { textSearchAdapter } = textSearching;
+            return textSearchAdapter;
+        });
+        return trackAdapters;
     }
     /**
      * Returns list of relevant results given a search query and options
      * @param args - search options/arguments include: search query
      * limit of results to return, searchType...prefix | full | exact", etc.
      */
-
-  }, {
-    key: "search",
-    value: function () {
-      var _search = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args, searchScope, rankFn) {
-        var textSearchAdapters, results;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                // determine list of relevant adapters based on scope
-                textSearchAdapters = this.loadTextSearchAdapters(searchScope);
-                _context.next = 3;
-                return Promise.all(textSearchAdapters.map(function (adapter) {
-                  return adapter.searchIndex(args);
-                }));
-
-              case 3:
-                results = _context.sent;
-                return _context.abrupt("return", this.sortResults(results.flat(), rankFn));
-
-              case 5:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function search(_x, _x2, _x3) {
-        return _search.apply(this, arguments);
-      }
-
-      return search;
-    }()
+    async search(args, searchScope, rankFn) {
+        // determine list of relevant adapters based on scope
+        const textSearchAdapters = this.loadTextSearchAdapters(searchScope);
+        const results = await Promise.all(textSearchAdapters.map(adapter => adapter.searchIndex(args)));
+        // aggregate and return relevant results
+        return this.sortResults(results.flat(), rankFn);
+    }
     /**
      * Returns array of revelevant and sorted results
      * @param results - array of results from all text search adapters
      * @param rankFn - function that updates results scores
      * based on more relevance
      */
-
-  }, {
-    key: "sortResults",
-    value: function sortResults(results, rankFn) {
-      return rankFn(results.sort(function (a, b) {
-        return -b.getLabel().localeCompare(a.getLabel());
-      })).sort(function (result1, result2) {
-        return result1.getScore() - result2.getScore();
-      });
+    sortResults(results, rankFn) {
+        return rankFn(results.sort((a, b) => -b.getLabel().localeCompare(a.getLabel()))).sort((result1, result2) => result1.getScore() - result2.getScore());
     }
-  }]);
-  return TextSearchManager;
-}();
-
-exports.default = TextSearchManager;
+}
+exports.default = TextSearchManager;