@jbrowse/react-app2 3.7.0 → 4.0.1

package/dist/rootModel/rootModel.js

@@ -1,166 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = RootModel;
-const app_core_1 = require("@jbrowse/app-core");
-const TextSearchManager_1 = __importDefault(require("@jbrowse/core/TextSearch/TextSearchManager"));
-const assemblyConfigSchema_1 = __importDefault(require("@jbrowse/core/assemblyManager/assemblyConfigSchema"));
-const RpcManager_1 = __importDefault(require("@jbrowse/core/rpc/RpcManager"));
-const Icons_1 = require("@jbrowse/core/ui/Icons");
-const product_core_1 = require("@jbrowse/product-core");
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-const GetApp_1 = __importDefault(require("@mui/icons-material/GetApp"));
-const Publish_1 = __importDefault(require("@mui/icons-material/Publish"));
-const Storage_1 = __importDefault(require("@mui/icons-material/Storage"));
-const file_saver_1 = require("file-saver");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const jbrowseModel_1 = __importDefault(require("../jbrowseModel"));
-const util_1 = require("../util");
-const version_1 = require("../version");
-function RootModel({ pluginManager, sessionModelFactory, makeWorkerInstance = () => {
-    throw new Error('no makeWorkerInstance supplied');
-}, }) {
-    const assemblyConfigSchema = (0, assemblyConfigSchema_1.default)(pluginManager);
-    return mobx_state_tree_1.types
-        .compose((0, product_core_1.BaseRootModelFactory)({
-        pluginManager,
-        jbrowseModelType: (0, jbrowseModel_1.default)({
-            pluginManager,
-            assemblyConfigSchema,
-        }),
-        sessionModelType: sessionModelFactory({
-            pluginManager,
-            assemblyConfigSchema,
-        }),
-        assemblyConfigSchema,
-    }), (0, product_core_1.InternetAccountsRootModelMixin)(pluginManager), (0, app_core_1.RootAppMenuMixin)())
-        .volatile(self => ({
-        version: version_1.version,
-        pluginsUpdated: false,
-        rpcManager: new RpcManager_1.default(pluginManager, self.jbrowse.configuration.rpc, {
-            WebWorkerRpcDriver: {
-                makeWorkerInstance,
-            },
-            MainThreadRpcDriver: {},
-        }),
-        textSearchManager: new TextSearchManager_1.default(pluginManager),
-        error: undefined,
-    }))
-        .actions(self => {
-        return {
-            afterCreate() {
-                (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                    if (self.pluginsUpdated) {
-                        window.location.reload();
-                    }
-                }));
-            },
-            setSession(sessionSnapshot) {
-                const oldSession = self.session;
-                self.session = (0, mobx_state_tree_1.cast)(sessionSnapshot);
-                if (self.session) {
-                    try {
-                        (0, util_1.filterSessionInPlace)(self.session, (0, mobx_state_tree_1.getType)(self.session));
-                    }
-                    catch (error) {
-                        self.session = oldSession;
-                        throw error;
-                    }
-                }
-            },
-            setPluginsUpdated(flag) {
-                self.pluginsUpdated = flag;
-            },
-            setDefaultSession() {
-                const { defaultSession } = self.jbrowse;
-                this.setSession({
-                    ...defaultSession,
-                    name: `${defaultSession.name} ${new Date().toLocaleString()}`,
-                });
-            },
-            renameCurrentSession(sessionName) {
-                if (self.session) {
-                    this.setSession({
-                        ...(0, mobx_state_tree_1.getSnapshot)(self.session),
-                        name: sessionName,
-                    });
-                }
-            },
-            setError(error) {
-                self.error = error;
-            },
-        };
-    })
-        .views(self => ({
-        menus() {
-            return (0, app_core_1.processMutableMenuActions)([
-                {
-                    label: 'File',
-                    menuItems: [
-                        {
-                            label: 'New session',
-                            icon: Add_1.default,
-                            onClick: (session) => {
-                                session.setDefaultSession();
-                            },
-                        },
-                        {
-                            label: 'Import session…',
-                            icon: Publish_1.default,
-                            onClick: (session) => {
-                                const widget = session.addWidget('ImportSessionWidget', 'importSessionWidget');
-                                session.showWidget(widget);
-                            },
-                        },
-                        {
-                            label: 'Export session',
-                            icon: GetApp_1.default,
-                            onClick: (session) => {
-                                const sessionBlob = new Blob([
-                                    JSON.stringify({ session: (0, mobx_state_tree_1.getSnapshot)(session) }, null, 2),
-                                ], { type: 'text/plain;charset=utf-8' });
-                                (0, file_saver_1.saveAs)(sessionBlob, 'session.json');
-                            },
-                        },
-                        { type: 'divider' },
-                        {
-                            label: 'Open track...',
-                            icon: Storage_1.default,
-                            onClick: (session) => {
-                                if (session.views.length === 0) {
-                                    session.notify('Please open a view to add a track first');
-                                }
-                                else if (session.views.length > 0) {
-                                    const widget = session.addWidget('AddTrackWidget', 'addTrackWidget', { view: session.views[0].id });
-                                    session.showWidget(widget);
-                                    if (session.views.length > 1) {
-                                        session.notify('This will add a track to the first view. Note: if you want to open a track in a specific view open the track selector for that view and use the add track (plus icon) in the bottom right');
-                                    }
-                                }
-                            },
-                        },
-                        {
-                            label: 'Open connection...',
-                            icon: Icons_1.Cable,
-                            onClick: (session) => {
-                                const widget = session.addWidget('AddConnectionWidget', 'addConnectionWidget');
-                                session.showWidget(widget);
-                            },
-                        },
-                    ],
-                },
-                {
-                    label: 'Add',
-                    menuItems: [],
-                },
-                {
-                    label: 'Tools',
-                    menuItems: [],
-                },
-            ], self.mutableMenuActions);
-        },
-    }));
-}

package/dist/rootModel/rootModel.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/rootModel/rootModel.test.js

@@ -1,140 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
-const mobx_state_tree_1 = require("mobx-state-tree");
-const corePlugins_1 = __importDefault(require("../corePlugins"));
-const rootModel_1 = __importDefault(require("./rootModel"));
-const sessionModel_1 = __importDefault(require("../sessionModel"));
-jest.mock('../makeWorkerInstance', () => () => { });
-function getRootModel() {
-    const pluginManager = new PluginManager_1.default(corePlugins_1.default.map(P => new P()));
-    pluginManager.createPluggableElements();
-    pluginManager.configure();
-    return (0, rootModel_1.default)({
-        pluginManager,
-        sessionModelFactory: sessionModel_1.default,
-    });
-}
-afterEach(() => {
-    localStorage.clear();
-    sessionStorage.clear();
-});
-const mainThreadConfig = {
-    jbrowse: {
-        configuration: {
-            rpc: {
-                defaultDriver: 'MainThreadRpcDriver',
-            },
-        },
-    },
-};
-test('creates with defaults', () => {
-    const root = getRootModel().create(mainThreadConfig);
-    expect(root.session).toBeUndefined();
-    root.setDefaultSession();
-    expect(root.session).toBeTruthy();
-    expect(root.jbrowse.assemblies.length).toBe(0);
-    expect((0, mobx_state_tree_1.getSnapshot)(root.jbrowse.configuration)).toMatchSnapshot();
-});
-test('creates with a minimal session', () => {
-    const root = getRootModel().create({
-        ...mainThreadConfig,
-        session: {
-            name: 'testSession',
-        },
-    });
-    expect(root.session).toBeTruthy();
-});
-test('activates a session snapshot', () => {
-    const session = { name: 'testSession' };
-    localStorage.setItem('localSaved-123', JSON.stringify({ session }));
-    Storage.prototype.getItem = jest.fn(() => `{"session": {"name": "testSession"}}`);
-    const root = getRootModel().create(mainThreadConfig);
-    expect(root.session).toBeUndefined();
-    root.setSession(session);
-    expect(root.session).toBeTruthy();
-});
-test('adds track and connection configs to an assembly', () => {
-    const root = getRootModel().create({
-        jbrowse: {
-            ...mainThreadConfig.jbrowse,
-            assemblies: [
-                {
-                    name: 'assembly1',
-                    aliases: ['assemblyA'],
-                    sequence: {
-                        trackId: 'sequenceConfigId',
-                        type: 'ReferenceSequenceTrack',
-                        adapter: {
-                            type: 'FromConfigSequenceAdapter',
-                            adapterId: 'sequenceConfigAdapterId',
-                            features: [
-                                {
-                                    refName: 'ctgA',
-                                    uniqueId: 'firstId',
-                                    start: 0,
-                                    end: 10,
-                                    seq: 'cattgttgcg',
-                                },
-                            ],
-                        },
-                    },
-                },
-            ],
-        },
-    });
-    expect(root.jbrowse.assemblies.length).toBe(1);
-    expect((0, mobx_state_tree_1.getSnapshot)(root.jbrowse.assemblies[0])).toMatchSnapshot();
-    const newTrackConf = root.jbrowse.addTrackConf({
-        type: 'FeatureTrack',
-        trackId: 'trackId0',
-    });
-    expect((0, mobx_state_tree_1.getSnapshot)(newTrackConf)).toMatchSnapshot();
-    expect(root.jbrowse.tracks.length).toBe(1);
-    const newConnectionConf = root.jbrowse.addConnectionConf({
-        type: 'JBrowse1Connection',
-        connectionId: 'connectionId0',
-    });
-    expect((0, mobx_state_tree_1.getSnapshot)(newConnectionConf)).toMatchSnapshot();
-    expect(root.jbrowse.connections.length).toBe(1);
-});
-test('throws if session is invalid', () => {
-    expect(() => {
-        getRootModel().create({
-            ...mainThreadConfig,
-            session: {},
-        });
-    }).toThrow();
-});
-test('throws if session snapshot is invalid', () => {
-    const root = getRootModel().create(mainThreadConfig);
-    expect(() => {
-        root.setSession({});
-    }).toThrow();
-});
-test('adds menus', () => {
-    const root = getRootModel().create(mainThreadConfig);
-    expect(root.menus()).toMatchSnapshot();
-    root.appendMenu('Third Menu');
-    root.insertMenu('Second Menu', -1);
-    root.appendToMenu('Second Menu', {
-        label: 'Second Menu Item',
-        onClick: () => { },
-    });
-    root.insertInMenu('Second Menu', {
-        label: 'First Menu Item',
-        onClick: () => { },
-    }, -1);
-    root.appendToSubMenu(['Second Menu', 'First Sub Menu'], {
-        label: 'Second Sub Menu Item',
-        onClick: () => { },
-    });
-    root.insertInSubMenu(['Second Menu', 'First Sub Menu'], {
-        label: 'First Sub Menu Item',
-        onClick: () => { },
-    }, -1);
-    expect(root.menus()).toMatchSnapshot();
-});

package/dist/rpcWorker.d.ts

@@ -1,2 +0,0 @@
-import './workerPolyfill';
-export default function doNothing(): void;

package/dist/rpcWorker.js

@@ -1,57 +0,0 @@
-"use strict";
-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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-var __rewriteRelativeImportExtension = (this && this.__rewriteRelativeImportExtension) || function (path, preserveJsx) {
-    if (typeof path === "string" && /^\.\.?\//.test(path)) {
-        return path.replace(/\.(tsx)$|((?:\.d)?)((?:\.[^./]+?)?)\.([cm]?)ts$/i, function (m, tsx, d, ext, cm) {
-            return tsx ? preserveJsx ? ".jsx" : ".js" : d && (!ext || !cm) ? m : (d + ext + "." + cm.toLowerCase() + "js");
-        });
-    }
-    return path;
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = doNothing;
-require("./workerPolyfill");
-const product_core_1 = require("@jbrowse/product-core");
-const mobx_react_1 = require("mobx-react");
-const corePlugins_1 = __importDefault(require("./corePlugins"));
-(0, mobx_react_1.enableStaticRendering)(true);
-(0, product_core_1.initializeWorker)(corePlugins_1.default, {
-    fetchESM: url => Promise.resolve(`${__rewriteRelativeImportExtension(url)}`).then(s => __importStar(require(s))),
-});
-function doNothing() {
-}