@jbrowse/plugin-legacy-jbrowse 1.7.9 → 2.0.0

package/dist/JBrowse1TextSeachAdapter/HttpMap.js

@@ -1,350 +1,205 @@
 "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 _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _bufferCrc = _interopRequireDefault(require("buffer-crc32"));
-
+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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
 /*
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */
-var HttpMap = /*#__PURE__*/function () {
-  function HttpMap(args) {
-    (0, _classCallCheck2.default)(this, HttpMap);
-    (0, _defineProperty2.default)(this, "url", void 0);
-    // make sure url has a trailing slash
-    this.url = /\/$/.test(args.url) ? args.url : "".concat(args.url, "/");
-  }
-  /**
-   * loads meta.json file from names directory and reads number of hash_bits used
-   */
-
-
-  (0, _createClass2.default)(HttpMap, [{
-    key: "readMeta",
-    value: function () {
-      var _readMeta = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-        var meta, compress, tracks, hashHexCharacters;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                _context.next = 2;
-                return this.loadFile('meta.json');
-
-              case 2:
-                meta = _context.sent;
-                compress = meta.compress, tracks = meta.track_names;
-                hashHexCharacters = Math.ceil(meta.hash_bits / 4);
-                return _context.abrupt("return", {
-                  hashHexCharacters: hashHexCharacters,
-                  compress: compress,
-                  tracks: tracks
-                });
-
-              case 6:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function readMeta() {
-        return _readMeta.apply(this, arguments);
-      }
-
-      return readMeta;
-    }()
-  }, {
-    key: "getHashHexCharacters",
-    value: function () {
-      var _getHashHexCharacters = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2() {
-        var meta;
-        return _regenerator.default.wrap(function _callee2$(_context2) {
-          while (1) {
-            switch (_context2.prev = _context2.next) {
-              case 0:
-                _context2.next = 2;
-                return this.readMeta();
-
-              case 2:
-                meta = _context2.sent;
-                return _context2.abrupt("return", meta.hashHexCharacters);
-
-              case 4:
-              case "end":
-                return _context2.stop();
-            }
-          }
-        }, _callee2, this);
-      }));
-
-      function getHashHexCharacters() {
-        return _getHashHexCharacters.apply(this, arguments);
-      }
-
-      return getHashHexCharacters;
-    }()
-  }, {
-    key: "getCompress",
-    value: function () {
-      var _getCompress = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee3() {
-        var meta;
-        return _regenerator.default.wrap(function _callee3$(_context3) {
-          while (1) {
-            switch (_context3.prev = _context3.next) {
-              case 0:
-                _context3.next = 2;
-                return this.readMeta();
-
-              case 2:
-                meta = _context3.sent;
-                return _context3.abrupt("return", meta.compress);
-
-              case 4:
-              case "end":
-                return _context3.stop();
-            }
-          }
-        }, _callee3, this);
-      }));
-
-      function getCompress() {
-        return _getCompress.apply(this, arguments);
-      }
-
-      return getCompress;
-    }()
-  }, {
-    key: "getTrackNames",
-    value: function () {
-      var _getTrackNames = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee4() {
-        var meta;
-        return _regenerator.default.wrap(function _callee4$(_context4) {
-          while (1) {
-            switch (_context4.prev = _context4.next) {
-              case 0:
-                _context4.next = 2;
-                return this.readMeta();
-
-              case 2:
-                meta = _context4.sent;
-                return _context4.abrupt("return", meta.tracks);
-
-              case 4:
-              case "end":
-                return _context4.stop();
-            }
-          }
-        }, _callee4, this);
-      }));
-
-      function getTrackNames() {
-        return _getTrackNames.apply(this, arguments);
-      }
-
-      return getTrackNames;
-    }()
+var buffer_crc32_1 = __importDefault(require("buffer-crc32"));
+var HttpMap = /** @class */ (function () {
+    function HttpMap(args) {
+        // make sure url has a trailing slash
+        this.url = /\/$/.test(args.url) ? args.url : "".concat(args.url, "/");
+    }
+    /**
+     * loads meta.json file from names directory and reads number of hash_bits used
+     */
+    HttpMap.prototype.readMeta = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var meta, compress, tracks, hashHexCharacters;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.loadFile('meta.json')];
+                    case 1:
+                        meta = _a.sent();
+                        compress = meta.compress, tracks = meta.track_names;
+                        hashHexCharacters = Math.ceil(meta.hash_bits / 4);
+                        return [2 /*return*/, { hashHexCharacters: hashHexCharacters, compress: compress, tracks: tracks }];
+                }
+            });
+        });
+    };
+    HttpMap.prototype.getHashHexCharacters = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var meta;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.readMeta()];
+                    case 1:
+                        meta = _a.sent();
+                        return [2 /*return*/, meta.hashHexCharacters];
+                }
+            });
+        });
+    };
+    HttpMap.prototype.getCompress = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var meta;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.readMeta()];
+                    case 1:
+                        meta = _a.sent();
+                        return [2 /*return*/, meta.compress];
+                }
+            });
+        });
+    };
+    HttpMap.prototype.getTrackNames = function () {
+        return __awaiter(this, void 0, void 0, function () {
+            var meta;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.readMeta()];
+                    case 1:
+                        meta = _a.sent();
+                        return [2 /*return*/, meta.tracks];
+                }
+            });
+        });
+    };
     /**
      * Returns contents of a bucket given a key
      * @param key - string
      */
-
-  }, {
-    key: "get",
-    value: function () {
-      var _get = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee5(key) {
-        var bucket;
-        return _regenerator.default.wrap(function _callee5$(_context5) {
-          while (1) {
-            switch (_context5.prev = _context5.next) {
-              case 0:
-                _context5.next = 2;
-                return this.getBucket(key);
-
-              case 2:
-                bucket = _context5.sent;
-                return _context5.abrupt("return", bucket[key]);
-
-              case 4:
-              case "end":
-                return _context5.stop();
-            }
-          }
-        }, _callee5, this);
-      }));
-
-      function get(_x) {
-        return _get.apply(this, arguments);
-      }
-
-      return get;
-    }()
+    HttpMap.prototype.get = function (key) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bucket;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getBucket(key)];
+                    case 1:
+                        bucket = _a.sent();
+                        return [2 /*return*/, bucket[key]];
+                }
+            });
+        });
+    };
     /**
      * Returns a bucket given a key
      * @param key - string
      */
-
-  }, {
-    key: "getBucket",
-    value: function () {
-      var _getBucket = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(key) {
-        var bucketIdent, hexToDirPath;
-        return _regenerator.default.wrap(function _callee6$(_context6) {
-          while (1) {
-            switch (_context6.prev = _context6.next) {
-              case 0:
-                bucketIdent = this.hash(key);
-                _context6.next = 3;
-                return this.hexToDirPath(bucketIdent);
-
-              case 3:
-                hexToDirPath = _context6.sent;
-                return _context6.abrupt("return", this.loadFile(hexToDirPath));
-
-              case 5:
-              case "end":
-                return _context6.stop();
-            }
-          }
-        }, _callee6, this);
-      }));
-
-      function getBucket(_x2) {
-        return _getBucket.apply(this, arguments);
-      }
-
-      return getBucket;
-    }()
+    HttpMap.prototype.getBucket = function (key) {
+        return __awaiter(this, void 0, void 0, function () {
+            var bucketIdent, hexToDirPath;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        bucketIdent = this.hash(key);
+                        return [4 /*yield*/, this.hexToDirPath(bucketIdent)];
+                    case 1:
+                        hexToDirPath = _a.sent();
+                        return [2 /*return*/, this.loadFile(hexToDirPath)];
+                }
+            });
+        });
+    };
     /**
      * Loads a file using the url and provided id.
      * Returns response object with contents of the file
      * @param id - string
      */
-
-  }, {
-    key: "loadFile",
-    value: function () {
-      var _loadFile = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(id) {
-        var response;
-        return _regenerator.default.wrap(function _callee7$(_context7) {
-          while (1) {
-            switch (_context7.prev = _context7.next) {
-              case 0:
-                _context7.next = 2;
-                return fetch("".concat(this.url).concat(id));
-
-              case 2:
-                response = _context7.sent;
-
-                if (response.ok) {
-                  _context7.next = 5;
-                  break;
+    HttpMap.prototype.loadFile = function (id) {
+        return __awaiter(this, void 0, void 0, function () {
+            var response;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, fetch("".concat(this.url).concat(id))];
+                    case 1:
+                        response = _a.sent();
+                        if (!response.ok) {
+                            throw new Error("HTTP ".concat(response.status, " ").concat(response.statusText));
+                        }
+                        return [2 /*return*/, response.json()];
                 }
-
-                throw new Error("HTTP ".concat(response.status, " ").concat(response.statusText));
-
-              case 5:
-                return _context7.abrupt("return", response.json());
-
-              case 6:
-              case "end":
-                return _context7.stop();
-            }
-          }
-        }, _callee7, this);
-      }));
-
-      function loadFile(_x3) {
-        return _loadFile.apply(this, arguments);
-      }
-
-      return loadFile;
-    }()
+            });
+        });
+    };
     /**
      * Returns the corresponding path of the file given a hex string
      * @param hex - hex string
      */
-
-  }, {
-    key: "hexToDirPath",
-    value: function () {
-      var _hexToDirPath = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(hex) {
-        var hashHexCharacters, compress, dirpath, i;
-        return _regenerator.default.wrap(function _callee8$(_context8) {
-          while (1) {
-            switch (_context8.prev = _context8.next) {
-              case 0:
-                _context8.next = 2;
-                return this.getHashHexCharacters();
-
-              case 2:
-                hashHexCharacters = _context8.sent;
-
-                if (!hashHexCharacters) {
-                  _context8.next = 12;
-                  break;
-                }
-
-                _context8.next = 6;
-                return this.getCompress();
-
-              case 6:
-                compress = _context8.sent;
-
-                while (hex.length < 8) {
-                  hex = "0".concat(hex);
-                }
-
-                hex = hex.substr(8 - hashHexCharacters);
-                dirpath = [];
-
-                for (i = 0; i < hex.length; i += 3) {
-                  dirpath.push(hex.substring(i, i + 3));
+    HttpMap.prototype.hexToDirPath = function (hex) {
+        return __awaiter(this, void 0, void 0, function () {
+            var hashHexCharacters, compress, dirpath, i;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0: return [4 /*yield*/, this.getHashHexCharacters()];
+                    case 1:
+                        hashHexCharacters = _a.sent();
+                        if (!hashHexCharacters) return [3 /*break*/, 3];
+                        return [4 /*yield*/, this.getCompress()];
+                    case 2:
+                        compress = _a.sent();
+                        while (hex.length < 8) {
+                            hex = "0".concat(hex);
+                        }
+                        hex = hex.substr(8 - hashHexCharacters);
+                        dirpath = [];
+                        for (i = 0; i < hex.length; i += 3) {
+                            dirpath.push(hex.substring(i, i + 3));
+                        }
+                        return [2 /*return*/, "".concat(dirpath.join('/'), ".json").concat(compress ? 'z' : '')];
+                    case 3: return [2 /*return*/, ''];
                 }
-
-                return _context8.abrupt("return", "".concat(dirpath.join('/'), ".json").concat(compress ? 'z' : ''));
-
-              case 12:
-                return _context8.abrupt("return", '');
-
-              case 13:
-              case "end":
-                return _context8.stop();
-            }
-          }
-        }, _callee8, this);
-      }));
-
-      function hexToDirPath(_x4) {
-        return _hexToDirPath.apply(this, arguments);
-      }
-
-      return hexToDirPath;
-    }()
-  }, {
-    key: "hash",
-    value: function hash(data) {
-      return (0, _bufferCrc.default)(Buffer.from(data)).toString('hex').toLowerCase().replace('-', 'n');
-    }
-  }]);
-  return HttpMap;
-}();
-
-exports.default = HttpMap;
+            });
+        });
+    };
+    HttpMap.prototype.hash = function (data) {
+        return (0, buffer_crc32_1.default)(Buffer.from(data))
+            .toString('hex')
+            .toLowerCase()
+            .replace('-', 'n');
+    };
+    return HttpMap;
+}());
+exports.default = HttpMap;
+//# sourceMappingURL=HttpMap.js.map

package/dist/JBrowse1TextSeachAdapter/HttpMap.js.map

@@ -0,0 +1 @@
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