@jbrowse/plugin-trix 1.7.11 → 2.0.0

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -1,191 +1,172 @@
 "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 _toArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toArray"));
-
-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 _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 _trix = _interopRequireDefault(require("@gmod/trix"));
-
-var _BaseAdapter2 = require("@jbrowse/core/data_adapters/BaseAdapter");
-
-var _io = require("@jbrowse/core/util/io");
-
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
-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 __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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var trix_1 = __importDefault(require("@gmod/trix"));
+var BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
+var io_1 = require("@jbrowse/core/util/io");
+var BaseResults_1 = __importDefault(require("@jbrowse/core/TextSearch/BaseResults"));
+var configuration_1 = require("@jbrowse/core/configuration");
 function decodeURIComponentNoThrow(uri) {
-  try {
-    return decodeURIComponent(uri);
-  } catch (e) {
-    // avoid throwing exception on a failure to decode URI component
-    return uri;
-  }
+    try {
+        return decodeURIComponent(uri);
+    }
+    catch (e) {
+        // avoid throwing exception on a failure to decode URI component
+        return uri;
+    }
 }
-
-function shorten(str, term) {
-  var w = arguments.length > 2 && arguments[2] !== undefined ? arguments[2] : 15;
-  var tidx = str.toLowerCase().indexOf(term);
-  return str.length < 40 ? str : (Math.max(0, tidx - w) > 0 ? '...' : '') + str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() + (tidx + term.length < str.length ? '...' : '');
+function shorten(str, term, w) {
+    if (w === void 0) { w = 15; }
+    var tidx = str.toLowerCase().indexOf(term);
+    return str.length < 40
+        ? str
+        : (Math.max(0, tidx - w) > 0 ? '...' : '') +
+            str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +
+            (tidx + term.length < str.length ? '...' : '');
 }
-
-var TrixTextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  (0, _inherits2.default)(TrixTextSearchAdapter, _BaseAdapter);
-
-  var _super = _createSuper(TrixTextSearchAdapter);
-
-  function TrixTextSearchAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, TrixTextSearchAdapter);
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "indexingAttributes", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "trixJs", void 0);
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "tracksNames", void 0);
-    var ixFilePath = (0, _configuration.readConfObject)(config, 'ixFilePath');
-    var ixxFilePath = (0, _configuration.readConfObject)(config, 'ixxFilePath');
-
-    if (!ixFilePath) {
-      throw new Error('must provide out.ix');
+var TrixTextSearchAdapter = /** @class */ (function (_super) {
+    __extends(TrixTextSearchAdapter, _super);
+    function TrixTextSearchAdapter(config, getSubAdapter, pluginManager) {
+        var _this = _super.call(this, config, getSubAdapter, pluginManager) || this;
+        var ixFilePath = (0, configuration_1.readConfObject)(config, 'ixFilePath');
+        var ixxFilePath = (0, configuration_1.readConfObject)(config, 'ixxFilePath');
+        if (!ixFilePath) {
+            throw new Error('must provide out.ix');
+        }
+        if (!ixxFilePath) {
+            throw new Error('must provide out.ixx');
+        }
+        _this.trixJs = new trix_1.default((0, io_1.openLocation)(ixxFilePath), (0, io_1.openLocation)(ixFilePath), 1500);
+        return _this;
     }
-
-    if (!ixxFilePath) {
-      throw new Error('must provide out.ixx');
-    }
-
-    _this.trixJs = new _trix.default((0, _io.openLocation)(ixxFilePath), (0, _io.openLocation)(ixFilePath), 1500);
-    return _this;
-  }
-  /*
-   * Returns list of results
-   * @param args - search options/arguments include: search query
-   * limit of results to return, searchType...prefix | full | exact", etc.
-   */
-
-
-  (0, _createClass2.default)(TrixTextSearchAdapter, [{
-    key: "searchIndex",
-    value: function () {
-      var _searchIndex = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(args) {
-        var query, strs, results, formatted;
-        return _regenerator.default.wrap(function _callee$(_context) {
-          while (1) {
-            switch (_context.prev = _context.next) {
-              case 0:
-                query = args.queryString.toLowerCase();
-                strs = query.split(' ');
-                _context.next = 4;
-                return this.trixJs.search(query);
-
-              case 4:
-                results = _context.sent;
-                formatted = results // if multi-word search try to filter out relevant items
-                .filter(function (_ref) {
-                  var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-                      data = _ref2[1];
-
-                  return strs.every(function (r) {
-                    return decodeURIComponentNoThrow(data).toLowerCase().includes(r);
-                  });
-                }).map(function (_ref3) {
-                  var _ref4 = (0, _slicedToArray2.default)(_ref3, 2),
-                      term = _ref4[0],
-                      data = _ref4[1];
-
-                  var result = JSON.parse(data.replace(/\|/g, ','));
-
-                  var _result$map = result.map(function (record) {
-                    return decodeURIComponentNoThrow(record);
-                  }),
-                      _result$map2 = (0, _toArray2.default)(_result$map),
-                      loc = _result$map2[0],
-                      trackId = _result$map2[1],
-                      rest = _result$map2.slice(2);
-
-                  var labelFieldIdx = rest.findIndex(function (elt) {
-                    return !!elt;
-                  });
-                  var contextIdx = rest.map(function (elt) {
-                    return elt.toLowerCase();
-                  }).findIndex(function (f) {
-                    return f.indexOf(term.toLowerCase()) !== -1;
-                  });
-                  var labelField = rest[labelFieldIdx];
-                  var contextField = rest[contextIdx];
-                  var context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
-                  var label = shorten(labelField, term);
-                  var displayString = !context || label.toLowerCase() === context.toLowerCase() ? label : "".concat(label, " (").concat(context, ")");
-                  return new _BaseResults.default({
-                    locString: loc,
-                    label: labelField,
-                    displayString: displayString,
-                    matchedObject: result.map(function (record) {
-                      return decodeURIComponent(record);
-                    }),
-                    trackId: trackId
-                  });
-                });
-
-                if (!(args.searchType === 'exact')) {
-                  _context.next = 8;
-                  break;
+    /*
+     * Returns list of results
+     * @param args - search options/arguments include: search query
+     * limit of results to return, searchType...prefix | full | exact", etc.
+     */
+    TrixTextSearchAdapter.prototype.searchIndex = function (args) {
+        return __awaiter(this, void 0, void 0, function () {
+            var query, strs, results, formatted;
+            return __generator(this, function (_a) {
+                switch (_a.label) {
+                    case 0:
+                        query = args.queryString.toLowerCase();
+                        strs = query.split(' ');
+                        return [4 /*yield*/, this.trixJs.search(query)];
+                    case 1:
+                        results = _a.sent();
+                        formatted = results
+                            // if multi-word search try to filter out relevant items
+                            .filter(function (_a) {
+                            var _b = __read(_a, 2), data = _b[1];
+                            return strs.every(function (r) {
+                                return decodeURIComponentNoThrow(data).toLowerCase().includes(r);
+                            });
+                        })
+                            .map(function (_a) {
+                            var _b = __read(_a, 2), term = _b[0], data = _b[1];
+                            var result = JSON.parse(data.replace(/\|/g, ','));
+                            var _c = __read(result.map(function (record) {
+                                return decodeURIComponentNoThrow(record);
+                            })), loc = _c[0], trackId = _c[1], rest = _c.slice(2);
+                            var labelFieldIdx = rest.findIndex(function (elt) { return !!elt; });
+                            var contextIdx = rest
+                                .map(function (elt) { return elt.toLowerCase(); })
+                                .findIndex(function (f) { return f.indexOf(term.toLowerCase()) !== -1; });
+                            var labelField = rest[labelFieldIdx];
+                            var contextField = rest[contextIdx];
+                            var context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
+                            var label = shorten(labelField, term);
+                            var displayString = !context || label.toLowerCase() === context.toLowerCase()
+                                ? label
+                                : "".concat(label, " (").concat(context, ")");
+                            return new BaseResults_1.default({
+                                locString: loc,
+                                label: labelField,
+                                displayString: displayString,
+                                matchedObject: result.map(function (record) { return decodeURIComponent(record); }),
+                                trackId: trackId,
+                            });
+                        });
+                        if (args.searchType === 'exact') {
+                            return [2 /*return*/, formatted.filter(function (res) { return res.getLabel().toLowerCase() === args.queryString.toLowerCase(); })];
+                        }
+                        return [2 /*return*/, formatted];
                 }
-
-                return _context.abrupt("return", formatted.filter(function (res) {
-                  return res.getLabel().toLowerCase() === args.queryString.toLowerCase();
-                }));
-
-              case 8:
-                return _context.abrupt("return", formatted);
-
-              case 9:
-              case "end":
-                return _context.stop();
-            }
-          }
-        }, _callee, this);
-      }));
-
-      function searchIndex(_x) {
-        return _searchIndex.apply(this, arguments);
-      }
-
-      return searchIndex;
-    }()
-  }, {
-    key: "freeResources",
-    value: function freeResources() {}
-  }]);
-  return TrixTextSearchAdapter;
-}(_BaseAdapter2.BaseAdapter);
-
-exports.default = TrixTextSearchAdapter;
+            });
+        });
+    };
+    TrixTextSearchAdapter.prototype.freeResources = function () { };
+    return TrixTextSearchAdapter;
+}(BaseAdapter_1.BaseAdapter));
+exports.default = TrixTextSearchAdapter;
+//# sourceMappingURL=TrixTextSearchAdapter.js.map

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map

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

@@ -1,50 +1,31 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _default = (0, _configuration.ConfigurationSchema)('TrixTextSearchAdapter', {
-  ixFilePath: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: 'out.ix',
-      locationType: 'UriLocation'
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+exports.default = (0, configuration_1.ConfigurationSchema)('TrixTextSearchAdapter', {
+    ixFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'out.ix', locationType: 'UriLocation' },
+        description: 'the location of the trix ix file',
     },
-    description: 'the location of the trix ix file'
-  },
-  ixxFilePath: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: 'out.ixx',
-      locationType: 'UriLocation'
+    ixxFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'out.ixx', locationType: 'UriLocation' },
+        description: 'the location of the trix ixx file',
     },
-    description: 'the location of the trix ixx file'
-  },
-  metaFilePath: {
-    type: 'fileLocation',
-    defaultValue: {
-      uri: 'meta.json',
-      locationType: 'UriLocation'
+    metaFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'meta.json', locationType: 'UriLocation' },
+        description: 'the location of the metadata json file for the trix index',
     },
-    description: 'the location of the metadata json file for the trix index'
-  },
-  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/TrixTextSearchAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TrixTextSearchAdapter/configSchema.ts"],"names":[],"mappings":";;AAAA,6DAAiE;AAEjE,kBAAe,IAAA,mCAAmB,EAChC,uBAAuB,EACvB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,YAAY,EAAE,aAAa,EAAE;QAC5D,WAAW,EAAE,kCAAkC;KAChD;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,SAAS,EAAE,YAAY,EAAE,aAAa,EAAE;QAC7D,WAAW,EAAE,mCAAmC;KACjD;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;QAC/D,WAAW,EAAE,2DAA2D;KACzE;IACD,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,CACrE,CAAA"}

package/dist/TrixTextSearchAdapter/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 _TrixTextSearchAdapter.default;
-  }
-});
-Object.defineProperty(exports, "configSchema", {
-  enumerable: true,
-  get: function get() {
-    return _configSchema.default;
-  }
-});
-
-var _TrixTextSearchAdapter = _interopRequireDefault(require("./TrixTextSearchAdapter"));
-
-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 TrixTextSearchAdapter_1 = require("./TrixTextSearchAdapter");
+Object.defineProperty(exports, "AdapterClass", { enumerable: true, get: function () { return __importDefault(TrixTextSearchAdapter_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/TrixTextSearchAdapter/index.js.map

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

package/dist/index.js

@@ -1,69 +1,44 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-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 _TextSearchAdapterType = _interopRequireDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
-
-var _Plugin2 = _interopRequireDefault(require("@jbrowse/core/Plugin"));
-
-var _TrixTextSearchAdapter = require("./TrixTextSearchAdapter");
-
-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 _default = /*#__PURE__*/function (_Plugin) {
-  (0, _inherits2.default)(_default, _Plugin);
-
-  var _super = _createSuper(_default);
-
-  function _default() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, _default);
-
-    for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
-      args[_key] = arguments[_key];
+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 __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var TextSearchAdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/TextSearchAdapterType"));
+var Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
+var TrixTextSearchAdapter_1 = require("./TrixTextSearchAdapter");
+var default_1 = /** @class */ (function (_super) {
+    __extends(default_1, _super);
+    function default_1() {
+        var _this = _super !== null && _super.apply(this, arguments) || this;
+        _this.name = 'TrixPlugin';
+        return _this;
     }
-
-    _this = _super.call.apply(_super, [this].concat(args));
-    (0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "name", 'TrixPlugin');
-    return _this;
-  }
-
-  (0, _createClass2.default)(_default, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addTextSearchAdapterType(function () {
-        return new _TextSearchAdapterType.default({
-          name: 'TrixTextSearchAdapter',
-          configSchema: _TrixTextSearchAdapter.configSchema,
-          AdapterClass: _TrixTextSearchAdapter.AdapterClass,
-          description: 'Trix adapter'
+    default_1.prototype.install = function (pluginManager) {
+        pluginManager.addTextSearchAdapterType(function () {
+            return new TextSearchAdapterType_1.default({
+                name: 'TrixTextSearchAdapter',
+                configSchema: TrixTextSearchAdapter_1.configSchema,
+                AdapterClass: TrixTextSearchAdapter_1.AdapterClass,
+                description: 'Trix adapter',
+            });
         });
-      });
-    }
-  }]);
-  return _default;
-}(_Plugin2.default);
-
-exports.default = _default;
+    };
+    return default_1;
+}(Plugin_1.default));
+exports.default = default_1;
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,oHAA6F;AAC7F,gEAAyC;AAEzC,iEAGgC;AAEhC;IAA6B,6BAAM;IAAnC;QAAA,qEAcC;QAbC,UAAI,GAAG,YAAY,CAAA;;IAarB,CAAC;IAXC,2BAAO,GAAP,UAAQ,aAA4B;QAClC,aAAa,CAAC,wBAAwB,CACpC;YACE,OAAA,IAAI,+BAAqB,CAAC;gBACxB,IAAI,EAAE,uBAAuB;gBAC7B,YAAY,EAAE,oCAAuB;gBACrC,YAAY,EAAE,oCAA0B;gBACxC,WAAW,EAAE,cAAc;aAC5B,CAAC;QALF,CAKE,CACL,CAAA;IACH,CAAC;IACH,gBAAC;AAAD,CAAC,AAdD,CAA6B,gBAAM,GAclC"}

package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts

@@ -0,0 +1,14 @@
+import Trix from '@gmod/trix';
+import { BaseTextSearchAdapter, BaseArgs, BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import PluginManager from '@jbrowse/core/PluginManager';
+import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache';
+export default class TrixTextSearchAdapter extends BaseAdapter implements BaseTextSearchAdapter {
+    indexingAttributes?: string[];
+    trixJs: Trix;
+    tracksNames?: string[];
+    constructor(config: AnyConfigurationModel, getSubAdapter?: getSubAdapterType, pluginManager?: PluginManager);
+    searchIndex(args: BaseArgs): Promise<BaseResult[]>;
+    freeResources(): void;
+}

package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -0,0 +1,77 @@
+import Trix from '@gmod/trix';
+import { BaseAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { openLocation } from '@jbrowse/core/util/io';
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults';
+import { readConfObject, } from '@jbrowse/core/configuration';
+function decodeURIComponentNoThrow(uri) {
+    try {
+        return decodeURIComponent(uri);
+    }
+    catch (e) {
+        // avoid throwing exception on a failure to decode URI component
+        return uri;
+    }
+}
+function shorten(str, term, w = 15) {
+    const tidx = str.toLowerCase().indexOf(term);
+    return str.length < 40
+        ? str
+        : (Math.max(0, tidx - w) > 0 ? '...' : '') +
+            str.slice(Math.max(0, tidx - w), tidx + term.length + w).trim() +
+            (tidx + term.length < str.length ? '...' : '');
+}
+export default class TrixTextSearchAdapter extends BaseAdapter {
+    constructor(config, getSubAdapter, pluginManager) {
+        super(config, getSubAdapter, pluginManager);
+        const ixFilePath = readConfObject(config, 'ixFilePath');
+        const ixxFilePath = readConfObject(config, 'ixxFilePath');
+        if (!ixFilePath) {
+            throw new Error('must provide out.ix');
+        }
+        if (!ixxFilePath) {
+            throw new Error('must provide out.ixx');
+        }
+        this.trixJs = new Trix(openLocation(ixxFilePath), openLocation(ixFilePath), 1500);
+    }
+    /*
+     * Returns list of results
+     * @param args - search options/arguments include: search query
+     * limit of results to return, searchType...prefix | full | exact", etc.
+     */
+    async searchIndex(args) {
+        const query = args.queryString.toLowerCase();
+        const strs = query.split(' ');
+        const results = await this.trixJs.search(query);
+        const formatted = results
+            // if multi-word search try to filter out relevant items
+            .filter(([, data]) => strs.every(r => decodeURIComponentNoThrow(data).toLowerCase().includes(r)))
+            .map(([term, data]) => {
+            const result = JSON.parse(data.replace(/\|/g, ','));
+            const [loc, trackId, ...rest] = result.map(record => decodeURIComponentNoThrow(record));
+            const labelFieldIdx = rest.findIndex(elt => !!elt);
+            const contextIdx = rest
+                .map(elt => elt.toLowerCase())
+                .findIndex(f => f.indexOf(term.toLowerCase()) !== -1);
+            const labelField = rest[labelFieldIdx];
+            const contextField = rest[contextIdx];
+            const context = contextIdx !== -1 ? shorten(contextField, term) : undefined;
+            const label = shorten(labelField, term);
+            const displayString = !context || label.toLowerCase() === context.toLowerCase()
+                ? label
+                : `${label} (${context})`;
+            return new BaseResult({
+                locString: loc,
+                label: labelField,
+                displayString,
+                matchedObject: result.map(record => decodeURIComponent(record)),
+                trackId,
+            });
+        });
+        if (args.searchType === 'exact') {
+            return formatted.filter(res => res.getLabel().toLowerCase() === args.queryString.toLowerCase());
+        }
+        return formatted;
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=TrixTextSearchAdapter.js.map

package/esm/TrixTextSearchAdapter/TrixTextSearchAdapter.js.map

@@ -0,0 +1 @@
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package/esm/TrixTextSearchAdapter/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const _default: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+export default _default;

package/esm/TrixTextSearchAdapter/configSchema.js

@@ -0,0 +1,29 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+export default ConfigurationSchema('TrixTextSearchAdapter', {
+    ixFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'out.ix', locationType: 'UriLocation' },
+        description: 'the location of the trix ix file',
+    },
+    ixxFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'out.ixx', locationType: 'UriLocation' },
+        description: 'the location of the trix ixx file',
+    },
+    metaFilePath: {
+        type: 'fileLocation',
+        defaultValue: { uri: 'meta.json', locationType: 'UriLocation' },
+        description: 'the location of the metadata json file for the trix index',
+    },
+    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/esm/TrixTextSearchAdapter/configSchema.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/TrixTextSearchAdapter/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AAEjE,eAAe,mBAAmB,CAChC,uBAAuB,EACvB;IACE,UAAU,EAAE;QACV,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,YAAY,EAAE,aAAa,EAAE;QAC5D,WAAW,EAAE,kCAAkC;KAChD;IACD,WAAW,EAAE;QACX,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,SAAS,EAAE,YAAY,EAAE,aAAa,EAAE;QAC7D,WAAW,EAAE,mCAAmC;KACjD;IACD,YAAY,EAAE;QACZ,IAAI,EAAE,cAAc;QACpB,YAAY,EAAE,EAAE,GAAG,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE;QAC/D,WAAW,EAAE,2DAA2D;KACzE;IACD,MAAM,EAAE;QACN,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,+CAA+C;KAC7D;IACD,aAAa,EAAE;QACb,IAAI,EAAE,aAAa;QACnB,YAAY,EAAE,EAAE;QAChB,WAAW,EAAE,mDAAmD;KACjE;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,kBAAkB,EAAE,qBAAqB,EAAE,CACrE,CAAA"}

package/esm/TrixTextSearchAdapter/index.d.ts

@@ -0,0 +1,2 @@
+export { default as AdapterClass } from './TrixTextSearchAdapter';
+export { default as configSchema } from './configSchema';

package/esm/TrixTextSearchAdapter/index.js

@@ -0,0 +1,3 @@
+export { default as AdapterClass } from './TrixTextSearchAdapter';
+export { default as configSchema } from './configSchema';
+//# sourceMappingURL=index.js.map

package/esm/TrixTextSearchAdapter/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/TrixTextSearchAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,yBAAyB,CAAA;AACjE,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,gBAAgB,CAAA"}

package/esm/index.d.ts

@@ -0,0 +1,6 @@
+import Plugin from '@jbrowse/core/Plugin';
+import PluginManager from '@jbrowse/core/PluginManager';
+export default class extends Plugin {
+    name: string;
+    install(pluginManager: PluginManager): void;
+}

package/esm/index.js

@@ -0,0 +1,18 @@
+import TextSearchAdapterType from '@jbrowse/core/pluggableElementTypes/TextSearchAdapterType';
+import Plugin from '@jbrowse/core/Plugin';
+import { AdapterClass as TrixTextSearchAdapterClass, configSchema as trixAdapterConfigSchema, } from './TrixTextSearchAdapter';
+export default class extends Plugin {
+    constructor() {
+        super(...arguments);
+        this.name = 'TrixPlugin';
+    }
+    install(pluginManager) {
+        pluginManager.addTextSearchAdapterType(() => new TextSearchAdapterType({
+            name: 'TrixTextSearchAdapter',
+            configSchema: trixAdapterConfigSchema,
+            AdapterClass: TrixTextSearchAdapterClass,
+            description: 'Trix adapter',
+        }));
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,2DAA2D,CAAA;AAC7F,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,EACL,YAAY,IAAI,0BAA0B,EAC1C,YAAY,IAAI,uBAAuB,GACxC,MAAM,yBAAyB,CAAA;AAEhC,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAarB,CAAC;IAXC,OAAO,CAAC,aAA4B;QAClC,aAAa,CAAC,wBAAwB,CACpC,GAAG,EAAE,CACH,IAAI,qBAAqB,CAAC;YACxB,IAAI,EAAE,uBAAuB;YAC7B,YAAY,EAAE,uBAAuB;YACrC,YAAY,EAAE,0BAA0B;YACxC,WAAW,EAAE,cAAc;SAC5B,CAAC,CACL,CAAA;IACH,CAAC;CACF"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "1.7.11",
+  "version": "2.0.0",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",
@@ -20,24 +20,28 @@
   "main": "dist/index.js",
   "files": [
     "dist",
-    "src"
+    "src",
+    "esm"
   ],
   "scripts": {
-    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
+    "build": "npm-run-all build:*",
     "test": "cd ../..; jest plugins/trix",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build; yarn useDist",
     "postpack": "yarn useSrc",
     "useDist": "node ../../scripts/useDist.js",
     "useSrc": "node ../../scripts/useSrc.js",
-    "postbuild": "tsc --build tsconfig.build.json"
+    "prebuild": "npm run clean",
+    "build:esm": "tsc --build tsconfig.build.esm.json",
+    "build:es5": "tsc --build tsconfig.build.es5.json",
+    "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
-    "@material-ui/core": "^4.9.13",
-    "mobx": "^5.0.0",
-    "mobx-react": "^6.0.0",
-    "mobx-state-tree": "3.14.1",
+    "@mui/material": "^4.9.13",
+    "mobx": "^6.0.0",
+    "mobx-react": "^7.0.0",
+    "mobx-state-tree": "^5.0.0",
     "prop-types": "^15.0.0",
     "react": ">=16.8.0"
   },
@@ -48,5 +52,8 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "5c21beb48a21f08b0091d293f09ac99174c48f77"
+  "distModule": "esm/index.js",
+  "srcModule": "src/index.ts",
+  "module": "esm/index.js",
+  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
 }

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.test.js

@@ -1,76 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
-var _path = _interopRequireDefault(require("path"));
-
-var _TrixTextSearchAdapter = _interopRequireDefault(require("./TrixTextSearchAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch output files', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var rootTemplate, urlPath, args, adapter, results, results2, test2;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'volvox', 'trix').replace(/\\/g, '\\\\');
-          urlPath = decodeURI(new URL("file://".concat(rootTemplate)).href);
-          args = {
-            type: 'TrixTextSearchAdapter',
-            textSearchAdapterId: 'TrixTextSearchAdapterTest',
-            ixFilePath: {
-              uri: "".concat(urlPath, "/volvox.ix"),
-              locationType: 'UriLocation'
-            },
-            ixxFilePath: {
-              uri: "".concat(urlPath, "/volvox.ixx"),
-              locationType: 'UriLocation'
-            },
-            metaFilePath: {
-              uri: "".concat(urlPath, "/volvox_meta.json"),
-              locationType: 'UriLocation'
-            }
-          }; // create adapter
-
-          adapter = new _TrixTextSearchAdapter.default(_configSchema.default.create(args)); // prefix search
-
-          _context.next = 6;
-          return adapter.searchIndex({
-            queryString: 'apple'
-          });
-
-        case 6:
-          results = _context.sent;
-          // check results are of type BaseResult for prefix search
-          expect(results[0] instanceof _BaseResults.default).toBeTruthy();
-          expect(results[0].getLabel()).toEqual('Apple2');
-          expect(results[1].getLabel()).toEqual('Apple3'); // exact search
-
-          _context.next = 12;
-          return adapter.searchIndex({
-            queryString: 'apple3'
-          });
-
-        case 12:
-          results2 = _context.sent;
-          // check results are of type location for exact search
-          expect(results2.length).toEqual(1);
-          test2 = results2[0];
-          expect(test2 instanceof _BaseResults.default).toBeTruthy();
-          expect(test2.getLabel()).toEqual('Apple3');
-          expect(test2.getLocation()).toEqual('ctgA:17400..23000');
-
-        case 18:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));