@jbrowse/plugin-trix 1.6.9 → 1.7.3

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.d.ts

@@ -1,14 +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;
-}
+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/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.js

@@ -0,0 +1,191 @@
+"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; } }
+
+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) {
+  (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');
+    }
+
+    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;
+                }
+
+                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;

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.test.js

@@ -0,0 +1,76 @@
+"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);
+})));

package/dist/TrixTextSearchAdapter/configSchema.d.ts

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

package/dist/TrixTextSearchAdapter/configSchema.js

@@ -0,0 +1,50 @@
+"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'
+    },
+    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'
+});
+
+exports["default"] = _default;

package/dist/TrixTextSearchAdapter/index.d.ts

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

package/dist/TrixTextSearchAdapter/index.js

@@ -0,0 +1,23 @@
+"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"));

package/dist/index.d.ts

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

package/dist/index.js

@@ -1,8 +1,69 @@
+"use strict";
 
-'use strict'
+var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
 
-if (process.env.NODE_ENV === 'production') {
-  module.exports = require('./plugin-trix.cjs.production.min.js')
-} else {
-  module.exports = require('./plugin-trix.cjs.development.js')
-}
+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];
+    }
+
+    _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'
+        });
+      });
+    }
+  }]);
+  return _default;
+}(_Plugin2["default"]);
+
+exports["default"] = _default;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-trix",
-  "version": "1.6.9",
+  "version": "1.7.3",
   "description": "JBrowse 2 trix text search adapter",
   "keywords": [
     "jbrowse",
@@ -18,21 +18,19 @@
   "distMain": "dist/index.js",
   "srcMain": "src/index.ts",
   "main": "dist/index.js",
-  "distModule": "dist/plugin-trix.esm.js",
-  "module": "dist/plugin-trix.esm.js",
   "files": [
     "dist",
     "src"
   ],
   "scripts": {
-    "start": "tsdx watch --verbose --noClean",
-    "build": "tsdx build",
+    "build": "babel src --root-mode upward --out-dir dist --extensions .ts,.js,.tsx,.jsx",
     "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"
+    "useSrc": "node ../../scripts/useSrc.js",
+    "postbuild": "tsc --build tsconfig.build.json"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -49,5 +47,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "f6c3d4edfadc26f7ac635a2fa7259f50f0c7e5e3"
+  "gitHead": "09b13c85acf4ac68dd71ab23af87656c7552fdaf"
 }