@jbrowse/plugin-data-management 1.7.11 → 2.1.0

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

@@ -0,0 +1 @@
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package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="react" />
+import { AddTrackModel } from '../model';
+declare function AddTrackWorkflow({ model }: {
+    model: AddTrackModel;
+}): JSX.Element;
+declare const _default: typeof AddTrackWorkflow;
+export default _default;

package/dist/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -0,0 +1,222 @@
+"use strict";
+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;
+});
+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),
+    },
+    stepper: {
+        backgroundColor: theme.palette.background.default,
+    },
+    button: {
+        marginTop: theme.spacing(1),
+        marginRight: theme.spacing(1),
+    },
+    actionsContainer: {
+        marginBottom: theme.spacing(2),
+    },
+    stepContent: {
+        margin: theme.spacing(1),
+    },
+    alertContainer: {
+        padding: "".concat(theme.spacing(2), "px 0px ").concat(theme.spacing(2), "px 0px"),
+    },
+}); });
+var steps = ['Enter track data', 'Confirm track type'];
+function AddTrackWorkflow(_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 pluginManager = (0, mobx_state_tree_1.getEnv)(model).pluginManager;
+    var rootModel = pluginManager.rootModel;
+    var jobsManager = rootModel.jobsManager;
+    var session = (0, util_1.getSession)(model);
+    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:
+                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, attr, indexName, 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'),
+                ].join('');
+                assemblyInstance = session.assemblyManager.get(assembly);
+                if (trackAdapter && trackAdapter.type !== 'UNKNOWN') {
+                    session.addTrackConf({
+                        trackId: trackId,
+                        type: trackType,
+                        name: trackName,
+                        assemblyNames: [assembly],
+                        adapter: __assign(__assign({}, trackAdapter), { sequenceAdapter: (0, configuration_1.getConf)(assemblyInstance, ['sequence', 'adapter']) }),
+                    });
+                    if (model.view) {
+                        model.view.showTrack(trackId);
+                        if (util_1.isElectron &&
+                            textIndexTrack &&
+                            (0, util_1.supportedIndexingAdapters)(trackAdapter.type)) {
+                            attr = textIndexingConf || {
+                                attributes: ['Name', 'ID'],
+                                exclude: ['CDS', 'exon'],
+                            };
+                            indexName = trackName + '-index';
+                            newEntry = {
+                                indexingParams: __assign(__assign({}, attr), { assemblies: [assembly], tracks: [trackId], indexType: 'perTrack', name: indexName, timestamp: new Date().toISOString() }),
+                                name: indexName,
+                                cancelCallback: function () { return jobsManager.abortJob(); },
+                            };
+                            jobsManager.queueJob(newEntry);
+                        }
+                    }
+                    else {
+                        session.notify('Open a new view, or use the track selector in an existing view, to view this track', 'info');
+                    }
+                    model.clearData();
+                    session.hideWidget(model);
+                }
+                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;
+        }
+    }
+    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))); }))));
+}
+exports.default = (0, mobx_react_1.observer)(AddTrackWorkflow);
+//# sourceMappingURL=DefaultAddTrackWorkflow.js.map

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

@@ -0,0 +1 @@
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package/dist/AddTrackWidget/components/TrackSourceSelect.js

@@ -1,60 +1,33 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = void 0;
-
-var _react = _interopRequireDefault(require("react"));
-
-var _ui = require("@jbrowse/core/ui");
-
-var _core = require("@material-ui/core");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _mobxReact = require("mobx-react");
-
-var useStyles = (0, _core.makeStyles)(function (theme) {
-  return {
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var react_1 = __importDefault(require("react"));
+var ui_1 = require("@jbrowse/core/ui");
+var material_1 = require("@mui/material");
+var mui_1 = require("tss-react/mui");
+var mobx_state_tree_1 = require("mobx-state-tree");
+var mobx_react_1 = require("mobx-react");
+var useStyles = (0, mui_1.makeStyles)()(function (theme) { return ({
     paper: {
-      display: 'flex',
-      flexDirection: 'column',
-      padding: theme.spacing(1)
+        display: 'flex',
+        flexDirection: 'column',
+        padding: theme.spacing(1),
     },
     spacer: {
-      height: theme.spacing(8)
-    }
-  };
-});
-
-function TrackSourceSelect(_ref) {
-  var model = _ref.model;
-  var classes = useStyles();
-  var rootModel = (0, _mobxStateTree.getRoot)(model);
-  return /*#__PURE__*/_react.default.createElement(_core.Paper, {
-    className: classes.paper
-  }, /*#__PURE__*/_react.default.createElement(_ui.FileSelector, {
-    name: "Main file",
-    description: "",
-    location: model.trackData,
-    setLocation: model.setTrackData,
-    setName: model.setTrackName,
-    rootModel: rootModel
-  }), /*#__PURE__*/_react.default.createElement("div", {
-    className: classes.spacer
-  }), /*#__PURE__*/_react.default.createElement(_ui.FileSelector, {
-    name: "Index file",
-    description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.",
-    location: model.indexTrackData,
-    setLocation: model.setIndexTrackData,
-    setName: model.setTrackName,
-    rootModel: rootModel
-  }));
+        height: theme.spacing(8),
+    },
+}); });
+function TrackSourceSelect(_a) {
+    var model = _a.model;
+    var classes = useStyles().classes;
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any
+    var rootModel = (0, mobx_state_tree_1.getRoot)(model);
+    return (react_1.default.createElement(material_1.Paper, { className: classes.paper },
+        react_1.default.createElement(ui_1.FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }),
+        react_1.default.createElement("div", { className: classes.spacer }),
+        react_1.default.createElement(ui_1.FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, setName: model.setTrackName, rootModel: rootModel })));
 }
-
-var _default = (0, _mobxReact.observer)(TrackSourceSelect);
-
-exports.default = _default;
+exports.default = (0, mobx_react_1.observer)(TrackSourceSelect);
+//# sourceMappingURL=TrackSourceSelect.js.map

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

@@ -0,0 +1 @@
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package/dist/AddTrackWidget/index.js

@@ -1,21 +1,11 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.configSchema = void 0;
-Object.defineProperty(exports, "stateModelFactory", {
-  enumerable: true,
-  get: function get() {
-    return _model.default;
-  }
-});
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _model = _interopRequireDefault(require("./model"));
-
-var configSchema = (0, _configuration.ConfigurationSchema)('AddTrackWidget', {});
-exports.configSchema = configSchema;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.configSchema = exports.stateModelFactory = void 0;
+var configuration_1 = require("@jbrowse/core/configuration");
+var model_1 = require("./model");
+Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return __importDefault(model_1).default; } });
+exports.configSchema = (0, configuration_1.ConfigurationSchema)('AddTrackWidget', {});
+//# sourceMappingURL=index.js.map

package/dist/AddTrackWidget/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AddTrackWidget/index.js"],"names":[],"mappings":";;;;;;AAAA,6DAAiE;AAEjE,iCAAsD;AAA7C,2HAAA,OAAO,OAAqB;AACxB,QAAA,YAAY,GAAG,IAAA,mCAAmB,EAAC,gBAAgB,EAAE,EAAE,CAAC,CAAA"}