@jbrowse/core 1.7.11 → 2.1.0

package/pluggableElementTypes/renderers/FeatureRendererType.js

@@ -1,61 +1,15 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = exports.NewFeatureRendererType = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _get2 = _interopRequireDefault(require("@babel/runtime/helpers/get"));
-
-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 _operators = require("rxjs/operators");
-
-var _util = require("../../util");
-
-var _simpleFeature = _interopRequireDefault(require("../../util/simpleFeature"));
-
-var _dataAdapterCache = require("../../data_adapters/dataAdapterCache");
-
-var _ServerSideRendererType = _interopRequireDefault(require("./ServerSideRendererType"));
-
-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; }
-
-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 FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
-  (0, _inherits2.default)(FeatureRendererType, _ServerSideRendererTy);
-
-  var _super = _createSuper(FeatureRendererType);
-
-  function FeatureRendererType() {
-    (0, _classCallCheck2.default)(this, FeatureRendererType);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(FeatureRendererType, [{
-    key: "serializeArgsInClient",
-    value:
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const operators_1 = require("rxjs/operators");
+const util_1 = require("../../util");
+const simpleFeature_1 = __importDefault(require("../../util/simpleFeature"));
+const dataAdapterCache_1 = require("../../data_adapters/dataAdapterCache");
+const ServerSideRendererType_1 = __importDefault(require("./ServerSideRendererType"));
+const BaseAdapter_1 = require("../../data_adapters/BaseAdapter");
+class FeatureRendererType extends ServerSideRendererType_1.default {
     /**
      * replaces the `displayModel` param (which on the client is a MST model) with
      * a stub that only contains the `selectedFeature`, since this is the only
@@ -64,19 +18,17 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
      *
      * @param args - the arguments passed to render
      */
-    function serializeArgsInClient(args) {
-      var displayModel = args.displayModel,
-          regions = args.regions;
-
-      var serializedArgs = _objectSpread(_objectSpread({}, args), {}, {
-        displayModel: displayModel && {
-          id: displayModel.id,
-          selectedFeatureId: displayModel.selectedFeatureId
-        },
-        regions: JSON.parse(JSON.stringify(regions))
-      });
-
-      return (0, _get2.default)((0, _getPrototypeOf2.default)(FeatureRendererType.prototype), "serializeArgsInClient", this).call(this, serializedArgs);
+    serializeArgsInClient(args) {
+        const { displayModel, regions } = args;
+        const serializedArgs = {
+            ...args,
+            displayModel: displayModel && {
+                id: displayModel.id,
+                selectedFeatureId: displayModel.selectedFeatureId,
+            },
+            regions: JSON.parse(JSON.stringify(regions)),
+        };
+        return super.serializeArgsInClient(serializedArgs);
     }
     /**
      * Adds feature deserialization to base server-side result deserialization
@@ -84,23 +36,21 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
      * @param results - the results of the render
      * @param args - the arguments passed to render
      */
-
-  }, {
-    key: "deserializeResultsInClient",
-    value: function deserializeResultsInClient(result, args) {
-      var deserializedFeatures = new Map();
-      result.features.forEach(function (j) {
-        var f = _simpleFeature.default.fromJSON(j);
-
-        deserializedFeatures.set(String(f.id()), f);
-      });
-      var deserialized = (0, _get2.default)((0, _getPrototypeOf2.default)(FeatureRendererType.prototype), "deserializeResultsInClient", this).call(this, _objectSpread(_objectSpread({}, result), {}, {
-        features: deserializedFeatures
-      }), args);
-      return _objectSpread(_objectSpread({}, deserialized), {}, {
-        blockKey: args.blockKey,
-        features: deserializedFeatures
-      });
+    deserializeResultsInClient(result, args) {
+        const deserializedFeatures = new Map();
+        result.features.forEach(j => {
+            const f = simpleFeature_1.default.fromJSON(j);
+            deserializedFeatures.set(String(f.id()), f);
+        });
+        const deserialized = super.deserializeResultsInClient({
+            ...result,
+            features: deserializedFeatures,
+        }, args);
+        return {
+            ...deserialized,
+            blockKey: args.blockKey,
+            features: deserializedFeatures,
+        };
     }
     /**
      * Adds feature serialization to base server-side result serialization
@@ -109,17 +59,13 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
      * method
      * @param args - deserialized render args
      */
-
-  }, {
-    key: "serializeResultsInWorker",
-    value: function serializeResultsInWorker(result, args) {
-      var serialized = (0, _get2.default)((0, _getPrototypeOf2.default)(FeatureRendererType.prototype), "serializeResultsInWorker", this).call(this, result, args);
-      var features = result.features;
-      return _objectSpread(_objectSpread({}, serialized), {}, {
-        features: (0, _util.iterMap)(features.values(), function (f) {
-          return f.toJSON();
-        }, features.size)
-      });
+    serializeResultsInWorker(result, args) {
+        const serialized = super.serializeResultsInWorker(result, args);
+        const { features } = result;
+        return {
+            ...serialized,
+            features: (0, util_1.iterMap)(features.values(), f => f.toJSON(), features.size),
+        };
     }
     /**
      * will expand if soft clipping or feature glyphs are shown
@@ -127,11 +73,8 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
      * @param region - rendering region
      * @param _renderArgs - render args, unused, may be used in deriving classes
      */
-
-  }, {
-    key: "getExpandedRegion",
-    value: function getExpandedRegion(region, _renderArgs) {
-      return region;
+    getExpandedRegion(region, _renderArgs) {
+        return region;
     }
     /**
      * use the dataAdapter to fetch the features to be rendered
@@ -139,168 +82,59 @@ var FeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy) {
      * @param renderArgs -
      * @returns Map of features as `{ id => feature, ... }`
      */
-
-  }, {
-    key: "getFeatures",
-    value: function () {
-      var _getFeatures = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(renderArgs) {
-        var _this = this;
-
-        var signal, regions, sessionId, adapterConfig, _yield$getAdapter, dataAdapter, features, requestRegions, region, featureObservable, feats;
-
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                signal = renderArgs.signal, regions = renderArgs.regions, sessionId = renderArgs.sessionId, adapterConfig = renderArgs.adapterConfig;
-                _context.next = 3;
-                return (0, _dataAdapterCache.getAdapter)(this.pluginManager, sessionId, adapterConfig);
-
-              case 3:
-                _yield$getAdapter = _context.sent;
-                dataAdapter = _yield$getAdapter.dataAdapter;
-                features = new Map();
-
-                if (!(!regions || regions.length === 0)) {
-                  _context.next = 8;
-                  break;
-                }
-
-                return _context.abrupt("return", features);
-
-              case 8:
-                requestRegions = regions.map(function (r) {
-                  // make sure the requested region's start and end are integers, if
-                  // there is a region specification.
-                  var requestRegion = _objectSpread({}, r);
-
-                  if (requestRegion.start) {
-                    requestRegion.start = Math.floor(requestRegion.start);
-                  }
-
-                  if (requestRegion.end) {
-                    requestRegion.end = Math.ceil(requestRegion.end);
-                  }
-
-                  return requestRegion;
-                });
-                region = requestRegions[0];
-                featureObservable = requestRegions.length === 1 ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), // @ts-ignore
-                renderArgs) : // @ts-ignore
-                dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
-                _context.next = 13;
-                return featureObservable.pipe((0, _operators.toArray)()).toPromise();
-
-              case 13:
-                feats = _context.sent;
-                (0, _util.checkAbortSignal)(signal);
-                return _context.abrupt("return", new Map(feats.filter(function (feat) {
-                  return _this.featurePassesFilters(renderArgs, feat);
-                }).map(function (feat) {
-                  return [feat.id(), feat];
-                })));
-
-              case 16:
-              case "end":
-                return _context.stop();
+    async getFeatures(renderArgs) {
+        const { signal, regions, sessionId, adapterConfig } = renderArgs;
+        const { dataAdapter } = await (0, dataAdapterCache_1.getAdapter)(this.pluginManager, sessionId, adapterConfig);
+        if (!(0, BaseAdapter_1.isFeatureAdapter)(dataAdapter)) {
+            throw new Error('Adapter does not support retrieving features');
+        }
+        const features = new Map();
+        if (!regions || regions.length === 0) {
+            return features;
+        }
+        const requestRegions = regions.map((r) => {
+            // make sure the requested region's start and end are integers, if
+            // there is a region specification.
+            const requestRegion = { ...r };
+            if (requestRegion.start) {
+                requestRegion.start = Math.floor(requestRegion.start);
             }
-          }
-        }, _callee, this);
-      }));
-
-      function getFeatures(_x) {
-        return _getFeatures.apply(this, arguments);
-      }
-
-      return getFeatures;
-    }()
+            if (requestRegion.end) {
+                requestRegion.end = Math.ceil(requestRegion.end);
+            }
+            return requestRegion;
+        });
+        const region = requestRegions[0];
+        const featureObservable = requestRegions.length === 1
+            ? dataAdapter.getFeatures(this.getExpandedRegion(region, renderArgs), renderArgs)
+            : dataAdapter.getFeaturesInMultipleRegions(requestRegions, renderArgs);
+        const feats = await featureObservable.pipe((0, operators_1.toArray)()).toPromise();
+        (0, util_1.checkAbortSignal)(signal);
+        return new Map(feats
+            .filter(feat => this.featurePassesFilters(renderArgs, feat))
+            .map(feat => [feat.id(), feat]));
+    }
     /**
      * @param renderArgs -
      * @param feature -
      * @returns true if this feature passes all configured filters
      */
-
-  }, {
-    key: "featurePassesFilters",
-    value: function featurePassesFilters(renderArgs, feature) {
-      if (!renderArgs.filters) {
-        return true;
-      }
-
-      return renderArgs.filters.passes(feature, renderArgs);
+    featurePassesFilters(renderArgs, feature) {
+        if (!renderArgs.filters) {
+            return true;
+        }
+        return renderArgs.filters.passes(feature, renderArgs);
     }
     /**
      * gets features and renders
      *
      * @param props - render args
      */
-
-  }, {
-    key: "render",
-    value: function () {
-      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(props) {
-        var features, result;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.t0 = props.features;
-
-                if (_context2.t0) {
-                  _context2.next = 5;
-                  break;
-                }
-
-                _context2.next = 4;
-                return this.getFeatures(props);
-
-              case 4:
-                _context2.t0 = _context2.sent;
-
-              case 5:
-                features = _context2.t0;
-                _context2.next = 8;
-                return (0, _get2.default)((0, _getPrototypeOf2.default)(FeatureRendererType.prototype), "render", this).call(this, _objectSpread(_objectSpread({}, props), {}, {
-                  features: features
-                }));
-
-              case 8:
-                result = _context2.sent;
-                return _context2.abrupt("return", _objectSpread(_objectSpread({}, result), {}, {
-                  features: features
-                }));
-
-              case 10:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function render(_x2) {
-        return _render.apply(this, arguments);
-      }
-
-      return render;
-    }()
-  }]);
-  return FeatureRendererType;
-}(_ServerSideRendererType.default);
-
+    async render(props) {
+        const features = props.features ||
+            (await this.getFeatures(props));
+        const result = await super.render({ ...props, features });
+        return { ...result, features };
+    }
+}
 exports.default = FeatureRendererType;
-
-var NewFeatureRendererType = /*#__PURE__*/function (_ServerSideRendererTy2) {
-  (0, _inherits2.default)(NewFeatureRendererType, _ServerSideRendererTy2);
-
-  var _super2 = _createSuper(NewFeatureRendererType);
-
-  function NewFeatureRendererType() {
-    (0, _classCallCheck2.default)(this, NewFeatureRendererType);
-    return _super2.apply(this, arguments);
-  }
-
-  return (0, _createClass2.default)(NewFeatureRendererType);
-}(_ServerSideRendererType.default);
-
-exports.NewFeatureRendererType = NewFeatureRendererType;

package/pluggableElementTypes/renderers/RendererType.js

@@ -1,113 +1,39 @@
 "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 _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _react = _interopRequireDefault(require("react"));
-
-var _mstReflection = require("../../util/mst-reflection");
-
-var _PluggableElementBase2 = _interopRequireDefault(require("../PluggableElementBase"));
-
-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 RendererType = /*#__PURE__*/function (_PluggableElementBase) {
-  (0, _inherits2.default)(RendererType, _PluggableElementBase);
-
-  var _super = _createSuper(RendererType);
-
-  function RendererType(stuff) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, RendererType);
-    _this = _super.call(this, stuff);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "ReactComponent", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "supportsSVG", false);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "configSchema", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "pluginManager", void 0);
-    _this.ReactComponent = stuff.ReactComponent;
-    _this.configSchema = stuff.configSchema;
-    _this.pluginManager = stuff.pluginManager;
-
-    if (!_this.ReactComponent) {
-      throw new Error("no ReactComponent defined for renderer ".concat(_this.name));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const mst_reflection_1 = require("../../util/mst-reflection");
+const PluggableElementBase_1 = __importDefault(require("../PluggableElementBase"));
+class RendererType extends PluggableElementBase_1.default {
+    constructor(stuff) {
+        super(stuff);
+        this.supportsSVG = false;
+        this.ReactComponent = stuff.ReactComponent;
+        this.configSchema = stuff.configSchema;
+        this.pluginManager = stuff.pluginManager;
+        if (!this.ReactComponent) {
+            throw new Error(`no ReactComponent defined for renderer ${this.name}`);
+        }
+        if (!(0, mst_reflection_1.getDefaultValue)(this.configSchema).type) {
+            throw new Error(`${this.name} config schema ${this.configSchema.name} is not explicitlyTyped`);
+        }
+        if (!this.pluginManager) {
+            throw new Error(`no plugin manager defined for renderer ${this.name}`);
+        }
     }
-
-    if (!(0, _mstReflection.getDefaultValue)(_this.configSchema).type) {
-      throw new Error("".concat(_this.name, " config schema ").concat(_this.configSchema.name, " is not explicitlyTyped"));
+    async render(props) {
+        return {
+            reactElement: react_1.default.createElement(this.ReactComponent, props, null),
+        };
     }
-
-    if (!_this.pluginManager) {
-      throw new Error("no plugin manager defined for renderer ".concat(_this.name));
-    }
-
-    return _this;
-  }
-
-  (0, _createClass2.default)(RendererType, [{
-    key: "render",
-    value: function () {
-      var _render = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(props) {
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                return _context.abrupt("return", {
-                  reactElement: /*#__PURE__*/_react.default.createElement(this.ReactComponent, props, null)
-                });
-
-              case 1:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function render(_x) {
-        return _render.apply(this, arguments);
-      }
-
-      return render;
-    }()
     /**
      * frees resources associated with the given range, session, etc.
      * optionally returns the number of data items deleted
      */
-
-  }, {
-    key: "freeResources",
-    value: function
-      /* specification: {} */
-    freeResources() {
-      return 0;
+    freeResources( /* specification: {} */) {
+        return 0;
     }
-  }]);
-  return RendererType;
-}(_PluggableElementBase2.default);
-
-exports.default = RendererType;
+}
+exports.default = RendererType;