@jbrowse/plugin-data-management 1.7.11 → 2.0.0

package/dist/AddTrackWidget/components/AddTrackWidget.js

@@ -1,251 +1,227 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _typeof = require("@babel/runtime/helpers/typeof");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
+var __assign = (this && this.__assign) || function () {
+    __assign = Object.assign || function(t) {
+        for (var s, i = 1, n = arguments.length; i < n; i++) {
+            s = arguments[i];
+            for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
+                t[p] = s[p];
+        }
+        return t;
+    };
+    return __assign.apply(this, arguments);
+};
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
 });
-exports.default = void 0;
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _defineProperty2 = _interopRequireDefault(require("@babel/runtime/helpers/defineProperty"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));
-
-var _react = _interopRequireWildcard(require("react"));
-
-var _core = require("@material-ui/core");
-
-var _util = require("@jbrowse/core/util");
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _mobxReact = require("mobx-react");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _lab = require("@material-ui/lab");
-
-var _ConfirmTrack = _interopRequireDefault(require("./ConfirmTrack"));
-
-var _TrackSourceSelect = _interopRequireDefault(require("./TrackSourceSelect"));
-
-function _getRequireWildcardCache(nodeInterop) { if (typeof WeakMap !== "function") return null; var cacheBabelInterop = new WeakMap(); var cacheNodeInterop = new WeakMap(); return (_getRequireWildcardCache = function _getRequireWildcardCache(nodeInterop) { return nodeInterop ? cacheNodeInterop : cacheBabelInterop; })(nodeInterop); }
-
-function _interopRequireWildcard(obj, nodeInterop) { if (!nodeInterop && obj && obj.__esModule) { return obj; } if (obj === null || _typeof(obj) !== "object" && typeof obj !== "function") { return { default: obj }; } var cache = _getRequireWildcardCache(nodeInterop); if (cache && cache.has(obj)) { return cache.get(obj); } var newObj = {}; var hasPropertyDescriptor = Object.defineProperty && Object.getOwnPropertyDescriptor; for (var key in obj) { if (key !== "default" && Object.prototype.hasOwnProperty.call(obj, key)) { var desc = hasPropertyDescriptor ? Object.getOwnPropertyDescriptor(obj, key) : null; if (desc && (desc.get || desc.set)) { Object.defineProperty(newObj, key, desc); } else { newObj[key] = obj[key]; } } } newObj.default = obj; if (cache) { cache.set(obj, newObj); } return newObj; }
-
-function ownKeys(object, enumerableOnly) { var keys = Object.keys(object); if (Object.getOwnPropertySymbols) { var symbols = Object.getOwnPropertySymbols(object); enumerableOnly && (symbols = symbols.filter(function (sym) { return Object.getOwnPropertyDescriptor(object, sym).enumerable; })), keys.push.apply(keys, symbols); } return keys; }
-
-function _objectSpread(target) { for (var i = 1; i < arguments.length; i++) { var source = null != arguments[i] ? arguments[i] : {}; i % 2 ? ownKeys(Object(source), !0).forEach(function (key) { (0, _defineProperty2.default)(target, key, source[key]); }) : Object.getOwnPropertyDescriptors ? Object.defineProperties(target, Object.getOwnPropertyDescriptors(source)) : ownKeys(Object(source)).forEach(function (key) { Object.defineProperty(target, key, Object.getOwnPropertyDescriptor(source, key)); }); } return target; }
-
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  return {
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+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 react_1 = __importStar(require("react"));
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var util_1 = require("@jbrowse/core/util");
+var configuration_1 = require("@jbrowse/core/configuration");
+var mobx_react_1 = require("mobx-react");
+var mobx_state_tree_1 = require("mobx-state-tree");
+// locals
+var ConfirmTrack_1 = __importDefault(require("./ConfirmTrack"));
+var TrackSourceSelect_1 = __importDefault(require("./TrackSourceSelect"));
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     root: {
-      marginTop: theme.spacing(1)
+        marginTop: theme.spacing(1),
     },
     stepper: {
-      backgroundColor: theme.palette.background.default
+        backgroundColor: theme.palette.background.default,
     },
     button: {
-      marginTop: theme.spacing(1),
-      marginRight: theme.spacing(1)
+        marginTop: theme.spacing(1),
+        marginRight: theme.spacing(1),
     },
     actionsContainer: {
-      marginBottom: theme.spacing(2)
+        marginBottom: theme.spacing(2),
     },
     stepContent: {
-      margin: theme.spacing(1)
+        margin: theme.spacing(1),
     },
     alertContainer: {
-      padding: "".concat(theme.spacing(2), "px 0px ").concat(theme.spacing(2), "px 0px")
-    }
-  };
-});
+        padding: "".concat(theme.spacing(2), "px 0px ").concat(theme.spacing(2), "px 0px"),
+    },
+}); });
 var steps = ['Enter track data', 'Confirm track type'];
-
-function AddTrackWidget(_ref) {
-  var model = _ref.model;
-
-  var _useState = (0, _react.useState)(0),
-      _useState2 = (0, _slicedToArray2.default)(_useState, 2),
-      activeStep = _useState2[0],
-      setActiveStep = _useState2[1];
-
-  var classes = useStyles();
-  var session = (0, _util.getSession)(model);
-
-  var _getEnv = (0, _mobxStateTree.getEnv)(session),
-      pluginManager = _getEnv.pluginManager;
-
-  var rootModel = pluginManager.rootModel;
-  var jobsManager = rootModel.jobsManager;
-  var assembly = model.assembly,
-      trackAdapter = model.trackAdapter,
-      trackData = model.trackData,
-      trackName = model.trackName,
-      trackType = model.trackType,
-      textIndexTrack = model.textIndexTrack,
-      textIndexingConf = model.textIndexingConf;
-
-  var _useState3 = (0, _react.useState)(),
-      _useState4 = (0, _slicedToArray2.default)(_useState3, 2),
-      trackErrorMessage = _useState4[0],
-      setTrackErrorMessage = _useState4[1];
-
-  function getStepContent(step) {
-    switch (step) {
-      case 0:
-        return /*#__PURE__*/_react.default.createElement(_TrackSourceSelect.default, {
-          model: model
-        });
-
-      case 1:
-        return /*#__PURE__*/_react.default.createElement(_ConfirmTrack.default, {
-          model: model
-        });
-
-      default:
-        return /*#__PURE__*/_react.default.createElement(_core.Typography, null, "Unknown step");
-    }
-  }
-
-  function handleNext() {
-    return _handleNext.apply(this, arguments);
-  }
-
-  function _handleNext() {
-    _handleNext = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-      var trackId, assemblyInstance, textSearchingDefault, attr, indexName, indexingParams, newEntry;
-      return _regenerator.default.wrap(function _callee$(_context) {
-        while (1) {
-          switch (_context.prev = _context.next) {
+function AddTrackWidget(_a) {
+    var model = _a.model;
+    var _b = __read((0, react_1.useState)(0), 2), activeStep = _b[0], setActiveStep = _b[1];
+    var classes = useStyles().classes;
+    var session = (0, util_1.getSession)(model);
+    var pluginManager = (0, mobx_state_tree_1.getEnv)(session).pluginManager;
+    var rootModel = pluginManager.rootModel;
+    var jobsManager = rootModel.jobsManager;
+    var assembly = model.assembly, trackAdapter = model.trackAdapter, trackData = model.trackData, trackName = model.trackName, trackType = model.trackType, textIndexTrack = model.textIndexTrack, textIndexingConf = model.textIndexingConf;
+    var _c = __read((0, react_1.useState)(), 2), trackErrorMessage = _c[0], setTrackErrorMessage = _c[1];
+    function getStepContent(step) {
+        switch (step) {
             case 0:
-              if (!(activeStep !== steps.length - 1)) {
-                _context.next = 3;
-                break;
-              }
-
-              setActiveStep(activeStep + 1);
-              return _context.abrupt("return");
-
-            case 3:
-              trackId = "".concat(trackName.toLowerCase().replace(/ /g, '_'), "-").concat(Date.now()).concat(session.adminMode ? '' : '-sessionTrack');
-              assemblyInstance = session.assemblyManager.get(assembly);
-
-              if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
-                // @ts-ignore
-                session.addTrackConf({
-                  trackId: trackId,
-                  type: trackType,
-                  name: trackName,
-                  assemblyNames: [assembly],
-                  adapter: _objectSpread(_objectSpread({}, trackAdapter), {}, {
-                    sequenceAdapter: (0, _configuration.getConf)(assemblyInstance, ['sequence', 'adapter'])
-                  })
-                });
-                textSearchingDefault = {
-                  attributes: ['Name', 'ID'],
-                  exclude: ['CDS', 'exon']
-                };
-
-                if (model.view) {
-                  model.view.showTrack(trackId);
-
-                  if (_util.isElectron) {
-                    if (textIndexTrack && (0, _util.supportedIndexingAdapters)(trackAdapter.type)) {
-                      attr = textIndexingConf || textSearchingDefault;
-                      indexName = trackName + '-index';
-                      indexingParams = _objectSpread(_objectSpread({}, attr), {}, {
-                        assemblies: [assembly],
-                        tracks: [trackId],
-                        indexType: 'perTrack',
-                        name: indexName,
-                        timestamp: new Date().toISOString()
-                      });
-                      newEntry = {
-                        indexingParams: indexingParams,
-                        name: indexName,
-                        cancelCallback: function cancelCallback() {
-                          jobsManager.abortJob();
+                return react_1.default.createElement(TrackSourceSelect_1.default, { model: model });
+            case 1:
+                return react_1.default.createElement(ConfirmTrack_1.default, { model: model });
+            default:
+                return react_1.default.createElement(material_1.Typography, null, "Unknown step");
+        }
+    }
+    function handleNext() {
+        return __awaiter(this, void 0, void 0, function () {
+            var trackId, assemblyInstance, textSearchingDefault, attr, indexName, indexingParams, newEntry;
+            return __generator(this, function (_a) {
+                if (activeStep !== steps.length - 1) {
+                    setActiveStep(activeStep + 1);
+                    return [2 /*return*/];
+                }
+                trackId = "".concat(trackName
+                    .toLowerCase()
+                    .replace(/ /g, '_'), "-").concat(Date.now()).concat(session.adminMode ? '' : '-sessionTrack');
+                assemblyInstance = session.assemblyManager.get(assembly);
+                if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
+                    // @ts-ignore
+                    session.addTrackConf({
+                        trackId: trackId,
+                        type: trackType,
+                        name: trackName,
+                        assemblyNames: [assembly],
+                        adapter: __assign(__assign({}, trackAdapter), { sequenceAdapter: (0, configuration_1.getConf)(assemblyInstance, ['sequence', 'adapter']) }),
+                    });
+                    textSearchingDefault = {
+                        attributes: ['Name', 'ID'],
+                        exclude: ['CDS', 'exon'],
+                    };
+                    if (model.view) {
+                        model.view.showTrack(trackId);
+                        if (util_1.isElectron) {
+                            if (textIndexTrack && (0, util_1.supportedIndexingAdapters)(trackAdapter.type)) {
+                                attr = textIndexingConf || textSearchingDefault;
+                                indexName = trackName + '-index';
+                                indexingParams = __assign(__assign({}, attr), { assemblies: [assembly], tracks: [trackId], indexType: 'perTrack', name: indexName, timestamp: new Date().toISOString() });
+                                newEntry = {
+                                    indexingParams: indexingParams,
+                                    name: indexName,
+                                    cancelCallback: function () {
+                                        jobsManager.abortJob();
+                                    },
+                                };
+                                jobsManager.queueJob(newEntry);
+                            }
                         }
-                      };
-                      jobsManager.queueJob(newEntry);
                     }
-                  }
-                } else {
-                  session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
+                    else {
+                        session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
+                    }
+                    model.clearData();
+                    // @ts-ignore
+                    session.hideWidget(model);
                 }
-
-                model.clearData(); // @ts-ignore
-
-                session.hideWidget(model);
-              } else {
-                setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
-              }
-
-            case 6:
-            case "end":
-              return _context.stop();
-          }
+                else {
+                    setTrackErrorMessage('Failed to add track.\nThe configuration of this file is not currently supported.');
+                }
+                return [2 /*return*/];
+            });
+        });
+    }
+    function handleBack() {
+        setTrackErrorMessage(undefined);
+        setActiveStep(activeStep - 1);
+    }
+    function isNextDisabled() {
+        switch (activeStep) {
+            case 0:
+                return !trackData;
+            case 1:
+                return !(trackName && trackType && (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) && assembly);
+            default:
+                return true;
         }
-      }, _callee);
-    }));
-    return _handleNext.apply(this, arguments);
-  }
-
-  function handleBack() {
-    setTrackErrorMessage(undefined);
-    setActiveStep(activeStep - 1);
-  }
-
-  function isNextDisabled() {
-    switch (activeStep) {
-      case 0:
-        return !trackData;
-
-      case 1:
-        return !(trackName && trackType && trackAdapter !== null && trackAdapter !== void 0 && trackAdapter.type && assembly);
-
-      default:
-        return true;
     }
-  }
-
-  return /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.root
-  }, /*#__PURE__*/_react.default.createElement(_core.Stepper, {
-    className: classes.stepper,
-    activeStep: activeStep,
-    orientation: "vertical"
-  }, steps.map(function (label, idx) {
-    return /*#__PURE__*/_react.default.createElement(_core.Step, {
-      key: label
-    }, /*#__PURE__*/_react.default.createElement(_core.StepLabel, null, label), /*#__PURE__*/_react.default.createElement(_core.StepContent, null, getStepContent(idx), /*#__PURE__*/_react.default.createElement("div", {
-      className: classes.actionsContainer
-    }, /*#__PURE__*/_react.default.createElement(_core.Button, {
-      disabled: activeStep === 0,
-      onClick: handleBack,
-      className: classes.button
-    }, "Back"), /*#__PURE__*/_react.default.createElement(_core.Button, {
-      disabled: isNextDisabled(),
-      variant: "contained",
-      color: "primary",
-      onClick: handleNext,
-      className: classes.button,
-      "data-testid": "addTrackNextButton"
-    }, activeStep === steps.length - 1 ? 'Add' : 'Next')), trackErrorMessage ? /*#__PURE__*/_react.default.createElement("div", {
-      className: classes.alertContainer
-    }, /*#__PURE__*/_react.default.createElement(_lab.Alert, {
-      severity: "error"
-    }, trackErrorMessage)) : null));
-  })));
+    return (react_1.default.createElement("div", { className: classes.root },
+        react_1.default.createElement(material_1.Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map(function (label, idx) { return (react_1.default.createElement(material_1.Step, { key: label },
+            react_1.default.createElement(material_1.StepLabel, null, label),
+            react_1.default.createElement(material_1.StepContent, null,
+                getStepContent(idx),
+                react_1.default.createElement("div", { className: classes.actionsContainer },
+                    react_1.default.createElement(material_1.Button, { disabled: activeStep === 0, onClick: handleBack, className: classes.button }, "Back"),
+                    react_1.default.createElement(material_1.Button, { disabled: isNextDisabled(), variant: "contained", color: "primary", onClick: handleNext, className: classes.button, "data-testid": "addTrackNextButton" }, activeStep === steps.length - 1 ? 'Add' : 'Next')),
+                trackErrorMessage ? (react_1.default.createElement("div", { className: classes.alertContainer },
+                    react_1.default.createElement(material_1.Alert, { severity: "error" }, trackErrorMessage))) : null))); }))));
 }
-
-var _default = (0, _mobxReact.observer)(AddTrackWidget);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(AddTrackWidget);
+//# sourceMappingURL=AddTrackWidget.js.map

package/dist/AddTrackWidget/components/AddTrackWidget.js.map

@@ -0,0 +1 @@
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