@jbrowse/plugin-config 1.7.11 → 2.1.0

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -1,127 +1,113 @@
 "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 _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-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 _inherits2 = _interopRequireDefault(require("@babel/runtime/helpers/inherits"));
-
-var _possibleConstructorReturn2 = _interopRequireDefault(require("@babel/runtime/helpers/possibleConstructorReturn"));
-
-var _getPrototypeOf2 = _interopRequireDefault(require("@babel/runtime/helpers/getPrototypeOf"));
-
-var _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-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 RefNameAliasAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(RefNameAliasAdapter, _BaseAdapter);
-
-  var _super = _createSuper(RefNameAliasAdapter);
-
-  function RefNameAliasAdapter() {
-    (0, _classCallCheck2.default)(this, RefNameAliasAdapter);
-    return _super.apply(this, arguments);
-  }
-
-  (0, _createClass2.default)(RefNameAliasAdapter, [{
-    key: "getRefNameAliases",
-    value: function () {
-      var _getRefNameAliases = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var loc, results, refColumn;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                loc = (0, _configuration.readConfObject)(this.config, 'location');
-
-                if (!(loc.uri === '' || loc.uri === '/path/to/my/aliases.txt')) {
-                  _context.next = 3;
-                  break;
-                }
-
-                return _context.abrupt("return", []);
-
-              case 3:
-                _context.next = 5;
-                return (0, _io.openLocation)(loc).readFile('utf8');
-
-              case 5:
-                results = _context.sent;
-                refColumn = (0, _configuration.readConfObject)(this.config, 'refNameColumn');
-                return _context.abrupt("return", results.trim().split('\n').filter(function (f) {
-                  return !!f && !f.startsWith('#');
-                }).map(function (row) {
-                  var aliases = row.split('\t');
-
-                  var _aliases$splice = aliases.splice(refColumn, 1),
-                      _aliases$splice2 = (0, _slicedToArray2.default)(_aliases$splice, 1),
-                      refName = _aliases$splice2[0];
-
-                  return {
-                    refName: refName,
-                    aliases: aliases.filter(function (f) {
-                      return !!f.trim();
-                    })
-                  };
-                }));
-
-              case 8:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function getRefNameAliases() {
-        return _getRefNameAliases.apply(this, arguments);
-      }
-
-      return getRefNameAliases;
-    }()
-  }, {
-    key: "freeResources",
-    value: function () {
-      var _freeResources = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-              case "end":
-                return _context2.stop();
+var __extends = (this && this.__extends) || (function () {
+    var extendStatics = function (d, b) {
+        extendStatics = Object.setPrototypeOf ||
+            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
+            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
+        return extendStatics(d, b);
+    };
+    return function (d, b) {
+        if (typeof b !== "function" && b !== null)
+            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
+        extendStatics(d, b);
+        function __() { this.constructor = d; }
+        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
+    };
+})();
+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;
             }
-          }
-        }, _callee2);
-      }));
-
-      function freeResources() {
-        return _freeResources.apply(this, arguments);
-      }
-
-      return freeResources;
-    }()
-  }]);
-  return RefNameAliasAdapter;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.default = RefNameAliasAdapter;
+            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 __read = (this && this.__read) || function (o, n) {
+    var m = typeof Symbol === "function" && o[Symbol.iterator];
+    if (!m) return o;
+    var i = m.call(o), r, ar = [], e;
+    try {
+        while ((n === void 0 || n-- > 0) && !(r = i.next()).done) ar.push(r.value);
+    }
+    catch (error) { e = { error: error }; }
+    finally {
+        try {
+            if (r && !r.done && (m = i["return"])) m.call(i);
+        }
+        finally { if (e) throw e.error; }
+    }
+    return ar;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var configuration_1 = require("@jbrowse/core/configuration");
+var RefNameAliasAdapter = /** @class */ (function (_super) {
+    __extends(RefNameAliasAdapter, _super);
+    function RefNameAliasAdapter() {
+        return _super !== null && _super.apply(this, arguments) || this;
+    }
+    RefNameAliasAdapter.prototype.getRefNameAliases = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var loc, results, refColumn;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        loc = (0, configuration_1.readConfObject)(this.config, 'location');
+                        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
+                            return [2 /*return*/, []];
+                        }
+                        return [4 /*yield*/, (0, io_1.openLocation)(loc).readFile('utf8')];
+                    case 1:
+                        results = _a.sent();
+                        refColumn = (0, configuration_1.readConfObject)(this.config, 'refNameColumn');
+                        return [2 /*return*/, results
+                                .trim()
+                                .split('\n')
+                                .filter(function (f) { return !!f && !f.startsWith('#'); })
+                                .map(function (row) {
+                                var aliases = row.split('\t');
+                                var _a = __read(aliases.splice(refColumn, 1), 1), refName = _a[0];
+                                return { refName: refName, aliases: aliases.filter(function (f) { return !!f.trim(); }) };
+                            })];
+                }
+            });
+        });
+    };
+    RefNameAliasAdapter.prototype.freeResources = function () {
+        return __awaiter(this, void 0, void 0, function () { return __generator(this, function (_a) {
+            return [2 /*return*/];
+        }); });
+    };
+    return RefNameAliasAdapter;
+}(BaseAdapter_1.BaseAdapter));
+exports.default = RefNameAliasAdapter;
+//# sourceMappingURL=RefNameAliasAdapter.js.map

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"RefNameAliasAdapter.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/RefNameAliasAdapter.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,uEAGgD;AAChD,4CAAoD;AACpD,6DAA4D;AAE5D;IACU,uCAAW;IADrB;;IAuBA,CAAC;IAnBO,+CAAiB,GAAvB;;;;;;wBACQ,GAAG,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,UAAU,CAAC,CAAA;wBACnD,IAAI,GAAG,CAAC,GAAG,KAAK,EAAE,IAAI,GAAG,CAAC,GAAG,KAAK,yBAAyB,EAAE;4BAC3D,sBAAO,EAAE,EAAA;yBACV;wBACe,qBAAM,IAAA,iBAAY,EAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAA;;wBAAlD,OAAO,GAAG,SAAwC;wBAClD,SAAS,GAAG,IAAA,8BAAc,EAAC,IAAI,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;wBAC9D,sBAAO,OAAO;iCACX,IAAI,EAAE;iCACN,KAAK,CAAC,IAAI,CAAC;iCACX,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,UAAU,CAAC,GAAG,CAAC,EAAzB,CAAyB,CAAC;iCACtC,GAAG,CAAC,UAAA,GAAG;gCACN,IAAM,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gCACzB,IAAA,KAAA,OAAY,OAAO,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,IAAA,EAAvC,OAAO,QAAgC,CAAA;gCAC9C,OAAO,EAAE,OAAO,SAAA,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,UAAA,CAAC,IAAI,OAAA,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,EAAV,CAAU,CAAC,EAAE,CAAA;4BAC9D,CAAC,CAAC,EAAA;;;;KACL;IAEK,2CAAa,GAAnB;;;;KAAwB;IAC1B,0BAAC;AAAD,CAAC,AAvBD,CACU,yBAAW,GAsBpB"}

package/dist/RefNameAliasAdapter/configSchema.js

@@ -1,26 +1,17 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('RefNameAliasAdapter', {
-  location: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/path/to/my/aliases.txt',
-      locationType: 'UriLocation'
-    }
-  },
-  refNameColumn: {
-    type: 'number',
-    defaultValue: 0
-  }
-}, {
-  explicitlyTyped: true
-});
-
-exports.default = _default;
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('RefNameAliasAdapter', {
+    location: {
+        type: 'fileLocation',
+        defaultValue: {
+            uri: '/path/to/my/aliases.txt',
+            locationType: 'UriLocation',
+        },
+    },
+    refNameColumn: {
+        type: 'number',
+        defaultValue: 0,
+    },
+}, { explicitlyTyped: true });
+//# sourceMappingURL=configSchema.js.map

package/dist/RefNameAliasAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,qBAAqB,EACrB;IACE,QAAQ,EAAE;QACR,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE;YACZ,GAAG,EAAE,yBAAyB;YAC9B,YAAY,EAAE,aAAa;SAC5B;KACF;IACD,aAAa,EAAE;QACb,IAAI,EAAE,QAAQ;QACd,YAAY,EAAE,CAAC;KAChB;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA"}

package/dist/RefNameAliasAdapter/index.js

@@ -1,23 +1,11 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-Object.defineProperty(exports, "AdapterClass", {
-  enumerable: true,
-  get: function get() {
-    return _RefNameAliasAdapter.default;
-  }
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _RefNameAliasAdapter = _interopRequireDefault(require("./RefNameAliasAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = exports.AdapterClass = void 0;
+var RefNameAliasAdapter_1 = require("./RefNameAliasAdapter");
+Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(RefNameAliasAdapter_1).default; } });
+var configSchema_1 = require("./configSchema");
+Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_1).default; } });
+//# sourceMappingURL=index.js.map

package/dist/RefNameAliasAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/RefNameAliasAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,6DAA+D;AAAtD,oIAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}

package/dist/index.d.ts

@@ -1,12 +1,18 @@
 /// <reference types="react" />
 import Plugin from '@jbrowse/core/Plugin';
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const ConfigurationEditorComponent: import("react").LazyExoticComponent<({ model }: {
-    model: any;
+declare const LazyConfigurationEditorComponent: import("react").LazyExoticComponent<({ model }: {
+    model: {
+        target: {
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: unknown): any;
+        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
+    };
 }) => JSX.Element>;
 export default class extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;
 }
 export { default as JsonEditor } from './ConfigurationEditorWidget/components/JsonEditor';
-export { ConfigurationEditorComponent as ConfigurationEditor };
+export { LazyConfigurationEditorComponent as ConfigurationEditor };