@jbrowse/plugin-legacy-jbrowse 1.7.9 → 2.0.0

package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js

@@ -1,191 +1,170 @@
 "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 _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));
-
-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 _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _HttpMap = _interopRequireDefault(require("./HttpMap"));
-
-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 __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;
+            }
+            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;
+};
+var __spreadArray = (this && this.__spreadArray) || function (to, from, pack) {
+    if (pack || arguments.length === 2) for (var i = 0, l = from.length, ar; i < l; i++) {
+        if (ar || !(i in from)) {
+            if (!ar) ar = Array.prototype.slice.call(from, 0, i);
+            ar[i] = from[i];
+        }
+    }
+    return to.concat(ar || Array.prototype.slice.call(from));
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+var configuration_1 = require("@jbrowse/core/configuration");
+var HttpMap_1 = __importDefault(require("./HttpMap"));
 //  Jbrowse1 text search adapter
 // Uses index built by generate-names.pl
-var JBrowse1TextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(JBrowse1TextSearchAdapter, _BaseAdapter);
-
-  var _super = _createSuper(JBrowse1TextSearchAdapter);
-
-  function JBrowse1TextSearchAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, JBrowse1TextSearchAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "httpMap", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "tracksNames", void 0);
-    var namesIndexLocation = (0, _configuration.readConfObject)(config, 'namesIndexLocation');
-
-    if (!namesIndexLocation) {
-      throw new Error('must provide namesIndexLocation');
+var JBrowse1TextSearchAdapter = /** @class */ (function (_super) {
+    __extends(JBrowse1TextSearchAdapter, _super);
+    function JBrowse1TextSearchAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var namesIndexLocation = (0, configuration_1.readConfObject)(config, 'namesIndexLocation');
+        if (!namesIndexLocation) {
+            throw new Error('must provide namesIndexLocation');
+        }
+        _this.httpMap = new HttpMap_1.default({
+            url: namesIndexLocation.baseUri
+                ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
+                : namesIndexLocation.uri,
+        });
+        return _this;
     }
-
-    _this.httpMap = new _HttpMap.default({
-      url: namesIndexLocation.baseUri ? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href : namesIndexLocation.uri
-    });
-    return _this;
-  }
-  /**
-   * Returns the contents of the file containing the query if it exists
-   * else it returns empty
-   * @param query - string query
-   */
-
-
-  (0, _createClass2.default)(JBrowse1TextSearchAdapter, [{
-    key: "loadIndexFile",
-    value: function () {
-      var _loadIndexFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(query) {
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                return _context.abrupt("return", this.httpMap.getBucket(query));
-
-              case 1:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function loadIndexFile(_x) {
-        return _loadIndexFile.apply(this, arguments);
-      }
-
-      return loadIndexFile;
-    }()
-  }, {
-    key: "searchIndex",
-    value: function () {
-      var _searchIndex = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(args) {
-        var searchType, queryString, tracks, entries;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                searchType = args.searchType, queryString = args.queryString;
-                _context2.t0 = this.tracksNames;
-
-                if (_context2.t0) {
-                  _context2.next = 6;
-                  break;
-                }
-
-                _context2.next = 5;
-                return this.httpMap.getTrackNames();
-
-              case 5:
-                _context2.t0 = _context2.sent;
-
-              case 6:
-                tracks = _context2.t0;
-                _context2.next = 9;
-                return this.loadIndexFile(queryString.toLowerCase());
-
-              case 9:
-                entries = _context2.sent;
-
-                if (!entries[queryString]) {
-                  _context2.next = 12;
-                  break;
-                }
-
-                return _context2.abrupt("return", this.formatResults(entries[queryString], tracks, searchType));
-
-              case 12:
-                return _context2.abrupt("return", []);
-
-              case 13:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function searchIndex(_x2) {
-        return _searchIndex.apply(this, arguments);
-      }
-
-      return searchIndex;
-    }()
-  }, {
-    key: "formatResults",
-    value: function formatResults(results, tracks, searchType) {
-      return [].concat((0, _toConsumableArray2.default)(searchType === 'exact' ? [] : results.prefix.map(function (result) {
-        return new _BaseResults.default({
-          label: (0, _typeof2.default)(result) === 'object' ? result.name : result,
-          matchedAttribute: 'name',
-          matchedObject: {
-            result: result
-          }
+    /**
+     * Returns the contents of the file containing the query if it exists
+     * else it returns empty
+     * @param query - string query
+     */
+    JBrowse1TextSearchAdapter.prototype.loadIndexFile = function (query) {
+        return __awaiter(this, void 0, void 0, function () {
+            return __generator(this, function (_a) {
+                return [2 /*return*/, this.httpMap.getBucket(query)];
+            });
         });
-      })), (0, _toConsumableArray2.default)(results.exact.map(function (result) {
-        var name = result[0];
-        var trackIndex = result[1];
-        var refName = result[3];
-        var start = result[4];
-        var end = result[5];
-        var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
-        return new _BaseResults.default({
-          locString: locstring,
-          label: name,
-          matchedAttribute: 'name',
-          matchedObject: result,
-          trackId: tracks[trackIndex]
+    };
+    JBrowse1TextSearchAdapter.prototype.searchIndex = function (args) {
+        return __awaiter(this, void 0, void 0, function () {
+            var searchType, queryString, tracks, _a, entries;
+            return __generator(this, function (_b) {
+                switch (_b.label) {
+                    case 0:
+                        searchType = args.searchType, queryString = args.queryString;
+                        _a = this.tracksNames;
+                        if (_a) return [3 /*break*/, 2];
+                        return [4 /*yield*/, this.httpMap.getTrackNames()];
+                    case 1:
+                        _a = (_b.sent());
+                        _b.label = 2;
+                    case 2:
+                        tracks = _a;
+                        return [4 /*yield*/, this.loadIndexFile(queryString.toLowerCase())];
+                    case 3:
+                        entries = _b.sent();
+                        if (entries[queryString]) {
+                            return [2 /*return*/, this.formatResults(entries[queryString], tracks, searchType)];
+                        }
+                        return [2 /*return*/, []];
+                }
+            });
         });
-      }))).filter(function (result) {
-        return result.getLabel() !== 'too many matches';
-      });
-    }
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return JBrowse1TextSearchAdapter;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.default = JBrowse1TextSearchAdapter;
+    };
+    JBrowse1TextSearchAdapter.prototype.formatResults = function (results, tracks, searchType) {
+        return __spreadArray(__spreadArray([], __read((searchType === 'exact'
+            ? []
+            : results.prefix.map(function (result) {
+                return new BaseResults_1.default({
+                    label: typeof result === 'object' ? result.name : result,
+                    matchedAttribute: 'name',
+                    matchedObject: { result: result },
+                });
+            }))), false), __read(results.exact.map(function (result) {
+            var name = result[0];
+            var trackIndex = result[1];
+            var refName = result[3];
+            var start = result[4];
+            var end = result[5];
+            var locstring = "".concat(refName || name, ":").concat(start, "-").concat(end);
+            return new BaseResults_1.default({
+                locString: locstring,
+                label: name,
+                matchedAttribute: 'name',
+                matchedObject: result,
+                trackId: tracks[trackIndex],
+            });
+        })), false).filter(function (result) { return result.getLabel() !== 'too many matches'; });
+    };
+    JBrowse1TextSearchAdapter.prototype.freeResources = function () { };
+    return JBrowse1TextSearchAdapter;
+}(BaseAdapter_1.BaseAdapter));
+exports.default = JBrowse1TextSearchAdapter;
+//# sourceMappingURL=JBrowse1TextSearchAdapter.js.map

package/dist/JBrowse1TextSeachAdapter/JBrowse1TextSearchAdapter.js.map

@@ -0,0 +1 @@
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package/dist/JBrowse1TextSeachAdapter/configSchema.js

@@ -1,35 +1,22 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('JBrowse1TextSearchAdapter', {
-  // metadata about tracks and assemblies covered by text search adapter
-  namesIndexLocation: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: '/volvox/names',
-      locationType: 'UriLocation'
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('JBrowse1TextSearchAdapter', {
+    // metadata about tracks and assemblies covered by text search adapter
+    namesIndexLocation: {
+        type: 'fileLocation',
+        defaultValue: { uri: '/volvox/names', locationType: 'UriLocation' },
+        description: 'the location of the JBrowse1 names index data directory',
     },
-    description: 'the location of the JBrowse1 names index data directory'
-  },
-  tracks: {
-    type: 'stringArray',
-    defaultValue: [],
-    description: 'List of tracks covered by text search adapter'
-  },
-  assemblyNames: {
-    type: 'stringArray',
-    defaultValue: [],
-    description: 'List of assemblies covered by text search adapter'
-  }
-}, {
-  explicitlyTyped: true,
-  explicitIdentifier: 'textSearchAdapterId'
-});
-
-exports.default = _default;
+    tracks: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of tracks covered by text search adapter',
+    },
+    assemblyNames: {
+        type: 'stringArray',
+        defaultValue: [],
+        description: 'List of assemblies covered by text search adapter',
+    },
+}, { explicitlyTyped: true, explicitIdentifier: 'textSearchAdapterId' });
+//# sourceMappingURL=configSchema.js.map

package/dist/JBrowse1TextSeachAdapter/configSchema.js.map

@@ -0,0 +1 @@
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package/dist/JBrowse1TextSeachAdapter/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 _JBrowse1TextSearchAdapter.default;
-  }
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _JBrowse1TextSearchAdapter = _interopRequireDefault(require("./JBrowse1TextSearchAdapter"));
-
-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 JBrowse1TextSearchAdapter_1 = require("./JBrowse1TextSearchAdapter");
+Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(JBrowse1TextSearchAdapter_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/JBrowse1TextSeachAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/JBrowse1TextSeachAdapter/index.ts"],"names":[],"mappings":";;;;;;AAAA,yEAAqE;AAA5D,0IAAA,OAAO,OAAgB;AAChC,+CAAwD;AAA/C,6HAAA,OAAO,OAAgB"}