@jbrowse/core 1.7.11 → 2.1.0

package/util/aborting.js

@@ -1,63 +1,9 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.abortBreakPoint = abortBreakPoint;
-exports.checkAbortSignal = checkAbortSignal;
-exports.isAbortException = isAbortException;
-exports.makeAbortError = makeAbortError;
-exports.observeAbortSignal = observeAbortSignal;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));
-
-var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));
-
-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 _wrapNativeSuper2 = _interopRequireDefault(require("@babel/runtime/helpers/wrapNativeSuper"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _rxjs = require("rxjs");
-
-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 AbortError = /*#__PURE__*/function (_Error) {
-  (0, _inherits2.default)(AbortError, _Error);
-
-  var _super = _createSuper(AbortError);
-
-  function AbortError() {
-    var _this;
-
-    (0, _classCallCheck2.default)(this, AbortError);
-
-    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), "code", void 0);
-    return _this;
-  }
-
-  return (0, _createClass2.default)(AbortError);
-}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.isAbortException = exports.observeAbortSignal = exports.makeAbortError = exports.abortBreakPoint = exports.checkAbortSignal = void 0;
+const rxjs_1 = require("rxjs");
+class AbortError extends Error {
+}
 /**
  * properly check if the given AbortSignal is aborted.
  * per the standard, if the signal reads as aborted,
@@ -69,90 +15,66 @@ var AbortError = /*#__PURE__*/function (_Error) {
  * @param signal -
  * @returns nothing
  */
-
-
 function checkAbortSignal(signal) {
-  if (!signal) {
-    return;
-  }
-
-  if (!(signal instanceof AbortSignal)) {
-    throw new TypeError('must pass an AbortSignal');
-  }
-
-  if (signal.aborted) {
-    throw makeAbortError();
-  }
+    if (!signal) {
+        return;
+    }
+    if (!(signal instanceof AbortSignal)) {
+        throw new TypeError('must pass an AbortSignal');
+    }
+    if (signal.aborted) {
+        throw makeAbortError();
+    }
 }
-
+exports.checkAbortSignal = checkAbortSignal;
 function timeout(ms) {
-  return new Promise(function (resolve) {
-    return setTimeout(resolve, ms);
-  });
+    return new Promise(resolve => setTimeout(resolve, ms));
 }
 /**
  * Skips to the next tick, then runs `checkAbortSignal`.
  * Await this to inside an otherwise synchronous loop to
  * provide a place to break when an abort signal is received.
  */
-
-
-function abortBreakPoint(_x) {
-  return _abortBreakPoint.apply(this, arguments);
-}
-
-function _abortBreakPoint() {
-  _abortBreakPoint = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(signal) {
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            _context.next = 2;
-            return timeout(1);
-
-          case 2:
-            checkAbortSignal(signal);
-
-          case 3:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee);
-  }));
-  return _abortBreakPoint.apply(this, arguments);
+async function abortBreakPoint(signal) {
+    // it was observed that an actual timeout is needed to get the aborting (wrap
+    // hicrenderer in a try catch, console.error the error, and rethrow the error
+    // to see). using await Promise.resolve() did not appear to allow aborting to
+    // occur
+    await timeout(1);
+    checkAbortSignal(signal);
 }
-
+exports.abortBreakPoint = abortBreakPoint;
 function makeAbortError() {
-  if (typeof DOMException !== 'undefined') {
-    return new DOMException('aborted', 'AbortError');
-  }
-
-  var e = new AbortError('aborted');
-  e.code = 'ERR_ABORTED';
-  return e;
+    if (typeof DOMException !== 'undefined') {
+        return new DOMException('aborted', 'AbortError');
+    }
+    const e = new AbortError('aborted');
+    e.code = 'ERR_ABORTED';
+    return e;
 }
-
+exports.makeAbortError = makeAbortError;
 function observeAbortSignal(signal) {
-  if (!signal) {
-    return _rxjs.Observable.create();
-  }
-
-  return (0, _rxjs.fromEvent)(signal, 'abort');
+    if (!signal) {
+        return rxjs_1.Observable.create();
+    }
+    return (0, rxjs_1.fromEvent)(signal, 'abort');
 }
+exports.observeAbortSignal = observeAbortSignal;
 /**
  * check if the given exception was caused by an operation being intentionally aborted
  * @param exception -
  */
-
-
 function isAbortException(exception) {
-  return exception instanceof Error && ( // DOMException
-  exception.name === 'AbortError' || // standard-ish non-DOM abort exception
-  exception.code === 'ERR_ABORTED' || // message contains aborted for bubbling through RPC
-  // things we have seen that we want to catch here
-  // Error: aborted
-  // AbortError: aborted
-  // AbortError: The user aborted a request.
-  !!exception.message.match(/\b(aborted|AbortError)\b/i));
-}
+    return (exception instanceof Error &&
+        // DOMException
+        (exception.name === 'AbortError' ||
+            // standard-ish non-DOM abort exception
+            exception.code === 'ERR_ABORTED' ||
+            // message contains aborted for bubbling through RPC
+            // things we have seen that we want to catch here
+            // Error: aborted
+            // AbortError: aborted
+            // AbortError: The user aborted a request.
+            !!exception.message.match(/\b(aborted|AbortError)\b/i)));
+}
+exports.isAbortException = isAbortException;

package/util/analytics.js

@@ -1,159 +1,96 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.doAnalytics = doAnalytics;
-exports.writeAWSAnalytics = writeAWSAnalytics;
-exports.writeGAAnalytics = writeGAAnalytics;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _configuration = require("../configuration");
-
-var _util = require("../util");
-
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.doAnalytics = exports.writeGAAnalytics = exports.writeAWSAnalytics = void 0;
 /* eslint-disable @typescript-eslint/no-explicit-any */
-function writeAWSAnalytics(_x, _x2, _x3) {
-  return _writeAWSAnalytics.apply(this, arguments);
-}
-
-function _writeAWSAnalytics() {
-  _writeAWSAnalytics = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(rootModel, initialTimeStamp, sessionQuery) {
-    var url, multiAssemblyTracks, savedSessionCount, config, session, ver, tracks, assemblies, plugins, stats, qs;
-    return _regenerator.default.wrap(function _callee$(_context) {
-      while (1) {
-        switch (_context.prev = _context.next) {
-          case 0:
-            _context.prev = 0;
-            url = 'https://analytics.jbrowse.org/api/v1';
-            multiAssemblyTracks = rootModel.jbrowse.tracks.filter(function (track) {
-              return ((0, _configuration.readConfObject)(track, 'assemblyNames') || []).length > 1;
-            }).length;
-            savedSessionCount = Object.keys(localStorage).filter(function (name) {
-              return name.includes('localSaved-');
-            }).length;
-            config = rootModel.jbrowse, session = rootModel.session, ver = rootModel.version;
-            tracks = config.tracks, assemblies = config.assemblies, plugins = config.plugins; // stats to be recorded in db
-
-            stats = {
-              ver: ver,
-              'plugins-count': (plugins === null || plugins === void 0 ? void 0 : plugins.length) || 0,
-              'plugin-names': plugins === null || plugins === void 0 ? void 0 : plugins.map(function (p) {
-                return p.name;
-              }).join(','),
-              'assemblies-count': assemblies.length,
-              'tracks-count': tracks.length,
-              'session-tracks-count': (session === null || session === void 0 ? void 0 : session.sessionTracks.length) || 0,
-              'open-views': (session === null || session === void 0 ? void 0 : session.views.length) || 0,
-              'synteny-tracks-count': multiAssemblyTracks,
-              'saved-sessions-count': savedSessionCount,
-              // field if existing session param in query before autogenerated param
-              'existing-session-param-type': (sessionQuery === null || sessionQuery === void 0 ? void 0 : sessionQuery.split('-')[0]) || 'none',
-              // screen geometry
-              'scn-h': window.screen.height,
-              'scn-w': window.screen.width,
-              // window geometry
-              'win-h': window.innerHeight,
-              'win-w': window.innerWidth,
-              electron: _util.isElectron,
-              loadTime: (Date.now() - initialTimeStamp) / 1000,
-              jb2: true
-            }; // stringifies the track type counts, gets processed in lambda
-
-            tracks.forEach(function (track) {
-              var key = "track-types-".concat(track.type);
-              stats[key] = stats[key] + 1 || 1;
-            }); // stringifies the session track type counts, gets processed in lambda
-
-            session === null || session === void 0 ? void 0 : session.sessionTracks.forEach(function (track) {
-              var key = "sessionTrack-types-".concat(track.type);
-              stats[key] = stats[key] + 1 || 1;
-            }); // put stats into a query string for get request
-
-            qs = Object.keys(stats).map(function (key) {
-              return "".concat(key, "=").concat(stats[key]);
-            }).join('&');
-            _context.next = 12;
-            return fetch("".concat(url, "?").concat(qs));
-
-          case 12:
-            _context.next = 17;
-            break;
-
-          case 14:
-            _context.prev = 14;
-            _context.t0 = _context["catch"](0);
-            console.error('Failed to write analytics to AWS.', _context.t0);
-
-          case 17:
-          case "end":
-            return _context.stop();
-        }
-      }
-    }, _callee, null, [[0, 14]]);
-  }));
-  return _writeAWSAnalytics.apply(this, arguments);
-}
-
-function writeGAAnalytics(_x4, _x5) {
-  return _writeGAAnalytics.apply(this, arguments);
+const configuration_1 = require("../configuration");
+const util_1 = require("../util");
+async function writeAWSAnalytics(rootModel, initialTimeStamp, sessionQuery) {
+    try {
+        const url = 'https://analytics.jbrowse.org/api/v1';
+        const multiAssemblyTracks = rootModel.jbrowse.tracks.filter((track) => ((0, configuration_1.readConfObject)(track, 'assemblyNames') || []).length > 1).length;
+        const savedSessionCount = Object.keys(localStorage).filter(name => name.includes('localSaved-')).length;
+        const { jbrowse: config, session, version: ver } = rootModel;
+        const { tracks, assemblies, plugins } = config;
+        // stats to be recorded in db
+        const stats = {
+            ver,
+            'plugins-count': (plugins === null || plugins === void 0 ? void 0 : plugins.length) || 0,
+            'plugin-names': plugins === null || plugins === void 0 ? void 0 : plugins.map((p) => p.name).join(','),
+            'assemblies-count': assemblies.length,
+            'tracks-count': tracks.length,
+            'session-tracks-count': (session === null || session === void 0 ? void 0 : session.sessionTracks.length) || 0,
+            'open-views': (session === null || session === void 0 ? void 0 : session.views.length) || 0,
+            'synteny-tracks-count': multiAssemblyTracks,
+            'saved-sessions-count': savedSessionCount,
+            // field if existing session param in query before autogenerated param
+            'existing-session-param-type': (sessionQuery === null || sessionQuery === void 0 ? void 0 : sessionQuery.split('-')[0]) || 'none',
+            // screen geometry
+            'scn-h': window.screen.height,
+            'scn-w': window.screen.width,
+            // window geometry
+            'win-h': window.innerHeight,
+            'win-w': window.innerWidth,
+            electron: util_1.isElectron,
+            loadTime: (Date.now() - initialTimeStamp) / 1000,
+            jb2: true,
+        };
+        // stringifies the track type counts, gets processed in lambda
+        tracks.forEach((track) => {
+            const key = `track-types-${track.type}`;
+            stats[key] = stats[key] + 1 || 1;
+        });
+        // stringifies the session track type counts, gets processed in lambda
+        session === null || session === void 0 ? void 0 : session.sessionTracks.forEach((track) => {
+            const key = `sessionTrack-types-${track.type}`;
+            stats[key] = stats[key] + 1 || 1;
+        });
+        // put stats into a query string for get request
+        const qs = Object.keys(stats)
+            .map(key => `${key}=${stats[key]}`)
+            .join('&');
+        await fetch(`${url}?${qs}`);
+    }
+    catch (e) {
+        console.error('Failed to write analytics to AWS.', e);
+    }
 }
-
-function _writeGAAnalytics() {
-  _writeGAAnalytics = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(rootModel, initialTimestamp) {
-    var _rootModel$jbrowse$pl;
-
-    var jbrowseUser, stats, analyticsScript, gaData, googleDimensions, analyticsScriptNode;
-    return _regenerator.default.wrap(function _callee2$(_context2) {
-      while (1) {
-        switch (_context2.prev = _context2.next) {
-          case 0:
-            jbrowseUser = 'UA-7115575-5';
-            stats = {
-              'tracks-count': rootModel.jbrowse.tracks.length,
-              // this is all possible tracks
-              ver: rootModel.version,
-              electron: _util.isElectron,
-              loadTime: Date.now() - initialTimestamp,
-              pluginNames: ((_rootModel$jbrowse$pl = rootModel.jbrowse.plugins) === null || _rootModel$jbrowse$pl === void 0 ? void 0 : _rootModel$jbrowse$pl.map(function (plugin) {
-                return plugin.name;
-              })) || ''
-            }; // create script
-
-            analyticsScript = "(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){";
-            analyticsScript += '(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),';
-            analyticsScript += 'm=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)';
-            analyticsScript += "})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');";
-            analyticsScript += "ga('create', '".concat(jbrowseUser, "', 'auto', 'jbrowseTracker');");
-            gaData = {};
-            googleDimensions = 'tracks-count ver electron loadTime pluginNames';
-            googleDimensions.split(/\s+/).forEach(function (key, index) {
-              gaData["dimension".concat(index + 1)] = stats[key];
-            });
-            gaData.metric1 = Math.round(stats.loadTime);
-            analyticsScript += "ga('jbrowseTracker.send', 'pageview',".concat(JSON.stringify(gaData), ");");
-            analyticsScriptNode = document.createElement('script');
-            analyticsScriptNode.innerHTML = analyticsScript;
-            document.getElementsByTagName('head')[0].appendChild(analyticsScriptNode);
-
-          case 15:
-          case "end":
-            return _context2.stop();
-        }
-      }
-    }, _callee2);
-  }));
-  return _writeGAAnalytics.apply(this, arguments);
+exports.writeAWSAnalytics = writeAWSAnalytics;
+async function writeGAAnalytics(rootModel, initialTimestamp) {
+    var _a;
+    const jbrowseUser = 'UA-7115575-5';
+    const stats = {
+        'tracks-count': rootModel.jbrowse.tracks.length,
+        ver: rootModel.version,
+        electron: util_1.isElectron,
+        loadTime: Date.now() - initialTimestamp,
+        pluginNames: ((_a = rootModel.jbrowse.plugins) === null || _a === void 0 ? void 0 : _a.map((plugin) => plugin.name)) || '',
+    };
+    // create script
+    let analyticsScript = "(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){";
+    analyticsScript +=
+        '(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),';
+    analyticsScript +=
+        'm=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)';
+    analyticsScript +=
+        "})(window,document,'script','https://www.google-analytics.com/analytics.js','ga');";
+    analyticsScript += `ga('create', '${jbrowseUser}', 'auto', 'jbrowseTracker');`;
+    const gaData = {};
+    const googleDimensions = 'tracks-count ver electron loadTime pluginNames';
+    googleDimensions.split(/\s+/).forEach((key, index) => {
+        gaData[`dimension${index + 1}`] = stats[key];
+    });
+    gaData.metric1 = Math.round(stats.loadTime);
+    analyticsScript += `ga('jbrowseTracker.send', 'pageview',${JSON.stringify(gaData)});`;
+    const analyticsScriptNode = document.createElement('script');
+    analyticsScriptNode.innerHTML = analyticsScript;
+    document.getElementsByTagName('head')[0].appendChild(analyticsScriptNode);
 }
-
+exports.writeGAAnalytics = writeGAAnalytics;
 function doAnalytics(rootModel, initialTimestamp, initialSessionQuery) {
-  if (rootModel && !(0, _configuration.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
-    writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
-    writeGAAnalytics(rootModel, initialTimestamp);
-  }
-}
+    if (rootModel &&
+        !(0, configuration_1.readConfObject)(rootModel.jbrowse.configuration, 'disableAnalytics')) {
+        writeAWSAnalytics(rootModel, initialTimestamp, initialSessionQuery);
+        writeGAAnalytics(rootModel, initialTimestamp);
+    }
+}
+exports.doAnalytics = doAnalytics;