@jbrowse/plugin-trix 1.7.0 → 1.7.4

package/dist/plugin-trix.cjs.development.js

@@ -1,1173 +0,0 @@
-'use strict';
-
-Object.defineProperty(exports, '__esModule', { value: true });
-
-function _interopDefault (ex) { return (ex && (typeof ex === 'object') && 'default' in ex) ? ex['default'] : ex; }
-
-var TextSearchAdapterType = _interopDefault(require('@jbrowse/core/pluggableElementTypes/TextSearchAdapterType'));
-var Plugin = _interopDefault(require('@jbrowse/core/Plugin'));
-var Trix = _interopDefault(require('@gmod/trix'));
-var BaseAdapter = require('@jbrowse/core/data_adapters/BaseAdapter');
-var io = require('@jbrowse/core/util/io');
-var BaseResult = _interopDefault(require('@jbrowse/core/TextSearch/BaseResults'));
-var configuration = require('@jbrowse/core/configuration');
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-function _unsupportedIterableToArray(o, minLen) {
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-function createCommonjsModule(fn, module) {
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-var runtime_1 = /*#__PURE__*/createCommonjsModule(function (module) {
-  /**
-   * Copyright (c) 2014-present, Facebook, Inc.
-   *
-   * This source code is licensed under the MIT license found in the
-   * LICENSE file in the root directory of this source tree.
-   */
-  var runtime = function (exports) {
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-    var Op = Object.prototype;
-    var hasOwn = Op.hasOwnProperty;
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-    var $Symbol = typeof Symbol === "function" ? Symbol : {};
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-    function wrap(innerFn, outerFn, self, tryLocsList) {
-      // If outerFn provided and outerFn.prototype is a Generator, then outerFn.prototype instanceof Generator.
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-      var generator = Object.create(protoGenerator.prototype);
-      var context = new Context(tryLocsList || []); // The ._invoke method unifies the implementations of the .next,
-      // .throw, and .return methods.
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-      generator._invoke = makeInvokeMethod(innerFn, self, context);
-      return generator;
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-
-    exports.wrap = wrap; // Try/catch helper to minimize deoptimizations. Returns a completion
-    // record like context.tryEntries[i].completion. This interface could
-    // have been (and was previously) designed to take a closure to be
-    // invoked without arguments, but in all the cases we care about we
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-    // in every case, so we don't have to touch the arguments object. The
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-    // has a stable shape and so hopefully should be cheap to allocate.
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-    function tryCatch(fn, obj, arg) {
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-
-    var GenStateSuspendedStart = "suspendedStart";
-    var GenStateSuspendedYield = "suspendedYield";
-    var GenStateExecuting = "executing";
-    var GenStateCompleted = "completed"; // Returning this object from the innerFn has the same effect as
-    // breaking out of the dispatch switch statement.
-
-    var ContinueSentinel = {}; // Dummy constructor functions that we use as the .constructor and
-    // .constructor.prototype properties for functions that return Generator
-    // objects. For full spec compliance, you may wish to configure your
-    // minifier not to mangle the names of these two functions.
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-    function Generator() {}
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-    if (NativeIteratorPrototype && NativeIteratorPrototype !== Op && hasOwn.call(NativeIteratorPrototype, iteratorSymbol)) {
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-    var Gp = GeneratorFunctionPrototype.prototype = Generator.prototype = Object.create(IteratorPrototype);
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-    define(GeneratorFunctionPrototype, "constructor", GeneratorFunction);
-    GeneratorFunction.displayName = define(GeneratorFunctionPrototype, toStringTagSymbol, "GeneratorFunction"); // Helper for defining the .next, .throw, and .return methods of the
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-    function defineIteratorMethods(prototype) {
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-    exports.isGeneratorFunction = function (genFun) {
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-      return ctor ? ctor === GeneratorFunction || // For the native GeneratorFunction constructor, the best we can
-      // do is to check its .name property.
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-    };
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-    exports.mark = function (genFun) {
-      if (Object.setPrototypeOf) {
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-      } else {
-        genFun.__proto__ = GeneratorFunctionPrototype;
-        define(genFun, toStringTagSymbol, "GeneratorFunction");
-      }
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-      genFun.prototype = Object.create(Gp);
-      return genFun;
-    }; // Within the body of any async function, `await x` is transformed to
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-
-    exports.awrap = function (arg) {
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-
-    function AsyncIterator(generator, PromiseImpl) {
-      function invoke(method, arg, resolve, reject) {
-        var record = tryCatch(generator[method], generator, arg);
-
-        if (record.type === "throw") {
-          reject(record.arg);
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-          var value = result.value;
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-          if (value && typeof value === "object" && hasOwn.call(value, "__await")) {
-            return PromiseImpl.resolve(value.__await).then(function (value) {
-              invoke("next", value, resolve, reject);
-            }, function (err) {
-              invoke("throw", err, resolve, reject);
-            });
-          }
-
-          return PromiseImpl.resolve(value).then(function (unwrapped) {
-            // When a yielded Promise is resolved, its final value becomes
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-            resolve(result);
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-      var previousPromise;
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-      function enqueue(method, arg) {
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-        return previousPromise = // If enqueue has been called before, then we want to wait until
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-        // call invoke immediately, without waiting on a callback to fire,
-        // so that the async generator function has the opportunity to do
-        // any necessary setup in a predictable way. This predictability
-        // is why the Promise constructor synchronously invokes its
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-        // execute code before the first await. Since we implement simple
-        // async functions in terms of async generators, it is especially
-        // important to get this right, even though it requires care.
-        previousPromise ? previousPromise.then(callInvokeWithMethodAndArg, // Avoid propagating failures to Promises returned by later
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-
-      this._invoke = enqueue;
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-    defineIteratorMethods(AsyncIterator.prototype);
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-    exports.AsyncIterator = AsyncIterator; // Note that simple async functions are implemented on top of
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-    // the final result produced by the iterator.
-
-    exports.async = function (innerFn, outerFn, self, tryLocsList, PromiseImpl) {
-      if (PromiseImpl === void 0) PromiseImpl = Promise;
-      var iter = new AsyncIterator(wrap(innerFn, outerFn, self, tryLocsList), PromiseImpl);
-      return exports.isGeneratorFunction(outerFn) ? iter // If outerFn is a generator, return the full iterator.
-      : iter.next().then(function (result) {
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-    function makeInvokeMethod(innerFn, self, context) {
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-
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-        context.method = method;
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-            context.method = "throw";
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-          context.method = "throw";
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-        return ContinueSentinel;
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-      var record = tryCatch(method, delegate.iterator, context.arg);
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-      if (record.type === "throw") {
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-      var info = record.arg;
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-      if (info.done) {
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-
-        context.next = delegate.nextLoc; // If context.method was "throw" but the delegate handled the
-        // exception, let the outer generator proceed normally. If
-        // context.method was "next", forget context.arg since it has been
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-        if (context.method !== "return") {
-          context.method = "next";
-          context.arg = undefined$1;
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-      context.delegate = null;
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-    } // Define Generator.prototype.{next,throw,return} in terms of the
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-    defineIteratorMethods(Gp);
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-    define(Gp, iteratorSymbol, function () {
-      return this;
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-    function pushTryEntry(locs) {
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-      if (1 in locs) {
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-      if (2 in locs) {
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-      this.tryEntries.push(entry);
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-    function resetTryEntry(entry) {
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-    exports.keys = function (object) {
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-      for (var key in object) {
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-      keys.reverse(); // Rather than returning an object with a next method, we keep
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-      return function next() {
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-    function values(iterable) {
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-        if (!isNaN(iterable.length)) {
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-            }
-
-            next.value = undefined$1;
-            next.done = true;
-            return next;
-          };
-
-          return next.next = next;
-        }
-      } // Return an iterator with no values.
-
-
-      return {
-        next: doneResult
-      };
-    }
-
-    exports.values = values;
-
-    function doneResult() {
-      return {
-        value: undefined$1,
-        done: true
-      };
-    }
-
-    Context.prototype = {
-      constructor: Context,
-      reset: function reset(skipTempReset) {
-        this.prev = 0;
-        this.next = 0; // Resetting context._sent for legacy support of Babel's
-        // function.sent implementation.
-
-        this.sent = this._sent = undefined$1;
-        this.done = false;
-        this.delegate = null;
-        this.method = "next";
-        this.arg = undefined$1;
-        this.tryEntries.forEach(resetTryEntry);
-
-        if (!skipTempReset) {
-          for (var name in this) {
-            // Not sure about the optimal order of these conditions:
-            if (name.charAt(0) === "t" && hasOwn.call(this, name) && !isNaN(+name.slice(1))) {
-              this[name] = undefined$1;
-            }
-          }
-        }
-      },
-      stop: function stop() {
-        this.done = true;
-        var rootEntry = this.tryEntries[0];
-        var rootRecord = rootEntry.completion;
-
-        if (rootRecord.type === "throw") {
-          throw rootRecord.arg;
-        }
-
-        return this.rval;
-      },
-      dispatchException: function dispatchException(exception) {
-        if (this.done) {
-          throw exception;
-        }
-
-        var context = this;
-
-        function handle(loc, caught) {
-          record.type = "throw";
-          record.arg = exception;
-          context.next = loc;
-
-          if (caught) {
-            // If the dispatched exception was caught by a catch block,
-            // then let that catch block handle the exception normally.
-            context.method = "next";
-            context.arg = undefined$1;
-          }
-
-          return !!caught;
-        }
-
-        for (var i = this.tryEntries.length - 1; i >= 0; --i) {
-          var entry = this.tryEntries[i];
-          var record = entry.completion;
-
-          if (entry.tryLoc === "root") {
-            // Exception thrown outside of any try block that could handle
-            // it, so set the completion value of the entire function to
-            // throw the exception.
-            return handle("end");
-          }
-
-          if (entry.tryLoc <= this.prev) {
-            var hasCatch = hasOwn.call(entry, "catchLoc");
-            var hasFinally = hasOwn.call(entry, "finallyLoc");
-
-            if (hasCatch && hasFinally) {
-              if (this.prev < entry.catchLoc) {
-                return handle(entry.catchLoc, true);
-              } else if (this.prev < entry.finallyLoc) {
-                return handle(entry.finallyLoc);
-              }
-            } else if (hasCatch) {
-              if (this.prev < entry.catchLoc) {
-                return handle(entry.catchLoc, true);
-              }
-            } else if (hasFinally) {
-              if (this.prev < entry.finallyLoc) {
-                return handle(entry.finallyLoc);
-              }
-            } else {
-              throw new Error("try statement without catch or finally");
-            }
-          }
-        }
-      },
-      abrupt: function abrupt(type, arg) {
-        for (var i = this.tryEntries.length - 1; i >= 0; --i) {
-          var entry = this.tryEntries[i];
-
-          if (entry.tryLoc <= this.prev && hasOwn.call(entry, "finallyLoc") && this.prev < entry.finallyLoc) {
-            var finallyEntry = entry;
-            break;
-          }
-        }
-
-        if (finallyEntry && (type === "break" || type === "continue") && finallyEntry.tryLoc <= arg && arg <= finallyEntry.finallyLoc) {
-          // Ignore the finally entry if control is not jumping to a
-          // location outside the try/catch block.
-          finallyEntry = null;
-        }
-
-        var record = finallyEntry ? finallyEntry.completion : {};
-        record.type = type;
-        record.arg = arg;
-
-        if (finallyEntry) {
-          this.method = "next";
-          this.next = finallyEntry.finallyLoc;
-          return ContinueSentinel;
-        }
-
-        return this.complete(record);
-      },
-      complete: function complete(record, afterLoc) {
-        if (record.type === "throw") {
-          throw record.arg;
-        }
-
-        if (record.type === "break" || record.type === "continue") {
-          this.next = record.arg;
-        } else if (record.type === "return") {
-          this.rval = this.arg = record.arg;
-          this.method = "return";
-          this.next = "end";
-        } else if (record.type === "normal" && afterLoc) {
-          this.next = afterLoc;
-        }
-
-        return ContinueSentinel;
-      },
-      finish: function finish(finallyLoc) {
-        for (var i = this.tryEntries.length - 1; i >= 0; --i) {
-          var entry = this.tryEntries[i];
-
-          if (entry.finallyLoc === finallyLoc) {
-            this.complete(entry.completion, entry.afterLoc);
-            resetTryEntry(entry);
-            return ContinueSentinel;
-          }
-        }
-      },
-      "catch": function _catch(tryLoc) {
-        for (var i = this.tryEntries.length - 1; i >= 0; --i) {
-          var entry = this.tryEntries[i];
-
-          if (entry.tryLoc === tryLoc) {
-            var record = entry.completion;
-
-            if (record.type === "throw") {
-              var thrown = record.arg;
-              resetTryEntry(entry);
-            }
-
-            return thrown;
-          }
-        } // The context.catch method must only be called with a location
-        // argument that corresponds to a known catch block.
-
-
-        throw new Error("illegal catch attempt");
-      },
-      delegateYield: function delegateYield(iterable, resultName, nextLoc) {
-        this.delegate = {
-          iterator: values(iterable),
-          resultName: resultName,
-          nextLoc: nextLoc
-        };
-
-        if (this.method === "next") {
-          // Deliberately forget the last sent value so that we don't
-          // accidentally pass it on to the delegate.
-          this.arg = undefined$1;
-        }
-
-        return ContinueSentinel;
-      }
-    }; // Regardless of whether this script is executing as a CommonJS module
-    // or not, return the runtime object so that we can declare the variable
-    // regeneratorRuntime in the outer scope, which allows this module to be
-    // injected easily by `bin/regenerator --include-runtime script.js`.
-
-    return exports;
-  }( // If this script is executing as a CommonJS module, use module.exports
-  // as the regeneratorRuntime namespace. Otherwise create a new empty
-  // object. Either way, the resulting object will be used to initialize
-  // the regeneratorRuntime variable at the top of this file.
-   module.exports );
-
-  try {
-    regeneratorRuntime = runtime;
-  } catch (accidentalStrictMode) {
-    // This module should not be running in strict mode, so the above
-    // assignment should always work unless something is misconfigured. Just
-    // in case runtime.js accidentally runs in strict mode, in modern engines
-    // we can explicitly access globalThis. In older engines we can escape
-    // strict mode using a global Function call. This could conceivably fail
-    // if a Content Security Policy forbids using Function, but in that case
-    // the proper solution is to fix the accidental strict mode problem. If
-    // you've misconfigured your bundler to force strict mode and applied a
-    // CSP to forbid Function, and you're not willing to fix either of those
-    // problems, please detail your unique predicament in a GitHub issue.
-    if (typeof globalThis === "object") {
-      globalThis.regeneratorRuntime = runtime;
-    } else {
-      Function("r", "regeneratorRuntime = r")(runtime);
-    }
-  }
-});
-
-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) {
-  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 ? '...' : '');
-}
-
-var TrixTextSearchAdapter = /*#__PURE__*/function (_BaseAdapter) {
-  _inherits(TrixTextSearchAdapter, _BaseAdapter);
-
-  var _super = /*#__PURE__*/_createSuper(TrixTextSearchAdapter);
-
-  function TrixTextSearchAdapter(config, getSubAdapter, pluginManager) {
-    var _this;
-
-    _classCallCheck(this, TrixTextSearchAdapter);
-
-    _this = _super.call(this, config, getSubAdapter, pluginManager);
-    var ixFilePath = configuration.readConfObject(config, 'ixFilePath');
-    var ixxFilePath = configuration.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(io.openLocation(ixxFilePath), 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.
-   */
-
-
-  _createClass(TrixTextSearchAdapter, [{
-    key: "searchIndex",
-    value: function () {
-      var _searchIndex = /*#__PURE__*/_asyncToGenerator( /*#__PURE__*/runtime_1.mark(function _callee(args) {
-        var query, strs, results, formatted;
-        return runtime_1.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 = _slicedToArray(_ref, 2),
-                      data = _ref2[1];
-
-                  return strs.every(function (r) {
-                    return decodeURIComponentNoThrow(data).toLowerCase().includes(r);
-                  });
-                }).map(function (_ref3) {
-                  var _ref4 = _slicedToArray(_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 = _toArray(_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 BaseResult({
-                    locString: loc,
-                    label: labelField,
-                    displayString: displayString,
-                    matchedObject: result.map(function (record) {
-                      return decodeURIComponent(record);
-                    }),
-                    trackId: trackId
-                  });
-                });
-
-                if (!(args.searchType === 'exact')) {
-                  _context.next = 8;
-                  break;
-                }
-
-                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;
-}(BaseAdapter.BaseAdapter);
-
-var trixAdapterConfigSchema = /*#__PURE__*/configuration.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'
-});
-
-var _default = /*#__PURE__*/function (_Plugin) {
-  _inherits(_default, _Plugin);
-
-  var _super = /*#__PURE__*/_createSuper(_default);
-
-  function _default() {
-    var _this;
-
-    _classCallCheck(this, _default);
-
-    _this = _super.apply(this, arguments);
-    _this.name = 'TrixPlugin';
-    return _this;
-  }
-
-  _createClass(_default, [{
-    key: "install",
-    value: function install(pluginManager) {
-      pluginManager.addTextSearchAdapterType(function () {
-        return new TextSearchAdapterType({
-          name: 'TrixTextSearchAdapter',
-          configSchema: trixAdapterConfigSchema,
-          AdapterClass: TrixTextSearchAdapter,
-          description: 'Trix adapter'
-        });
-      });
-    }
-  }]);
-
-  return _default;
-}(Plugin);
-
-exports.default = _default;
-//# sourceMappingURL=plugin-trix.cjs.development.js.map