@jbrowse/web-core 2.17.0 → 3.0.0

package/dist/BaseWebSession/index.js

@@ -15,182 +15,97 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.BaseWebSession = BaseWebSession;
 const react_1 = require("react");
-const clone_1 = __importDefault(require("clone"));
+const app_core_1 = require("@jbrowse/app-core");
 const configuration_1 = require("@jbrowse/core/configuration");
+const SnackbarModel_1 = __importDefault(require("@jbrowse/core/ui/SnackbarModel"));
 const util_1 = require("@jbrowse/core/util");
-const mobx_1 = require("mobx");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const product_core_1 = require("@jbrowse/product-core");
-const app_core_1 = require("@jbrowse/app-core");
-const SnackbarModel_1 = __importDefault(require("@jbrowse/core/ui/SnackbarModel"));
-// icons
-const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
-const FileCopy_1 = __importDefault(require("@mui/icons-material/FileCopy"));
 const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
+const FileCopy_1 = __importDefault(require("@mui/icons-material/FileCopy"));
 const Info_1 = __importDefault(require("@mui/icons-material/Info"));
-// locals
+const Settings_1 = __importDefault(require("@mui/icons-material/Settings"));
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
 const SessionConnections_1 = require("../SessionConnections");
-// lazies
 const AboutDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AboutDialog'))));
-/**
- * #stateModel BaseWebSession
- * used for "web based" products, including jbrowse-web and react-app
- * composed of
- * - [ReferenceManagementSessionMixin](../referencemanagementsessionmixin)
- * - [DrawerWidgetSessionMixin](../drawerwidgetsessionmixin)
- * - [DialogQueueSessionMixin](../dialogqueuesessionmixin)
- * - [ThemeManagerSessionMixin](../thememanagersessionmixin)
- * - [MultipleViewsSessionMixin](../multipleviewssessionmixin)
- * - [SessionTracksManagerSessionMixin](../sessiontracksmanagersessionmixin)
- * - [SessionAssembliesMixin](../sessionassembliesmixin)
- * - [TemporaryAssembliesMixin](../temporaryassembliesmixin)
- * - [WebSessionConnectionsMixin](../websessionconnectionsmixin)
- * - [AppFocusMixin](../appfocusmixin)
- */
 function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
     const sessionModel = mobx_state_tree_1.types
         .compose('WebCoreSessionModel', mobx_state_tree_1.types.compose('WebCoreSessionModelGroupA', (0, product_core_1.ReferenceManagementSessionMixin)(pluginManager), (0, product_core_1.DrawerWidgetSessionMixin)(pluginManager), (0, product_core_1.DialogQueueSessionMixin)(pluginManager), (0, product_core_1.ThemeManagerSessionMixin)(pluginManager), (0, product_core_1.MultipleViewsSessionMixin)(pluginManager)), mobx_state_tree_1.types.compose('WebCoreSessionModelGroupB', (0, product_core_1.SessionTracksManagerSessionMixin)(pluginManager), (0, app_core_1.SessionAssembliesMixin)(pluginManager, assemblyConfigSchema), (0, app_core_1.TemporaryAssembliesMixin)(pluginManager, assemblyConfigSchema), (0, SessionConnections_1.WebSessionConnectionsMixin)(pluginManager), (0, app_core_1.AppFocusMixin)(), (0, SnackbarModel_1.default)()))
         .props({
-        /**
-         * #property
-         */
         margin: 0,
-        /**
-         * #property
-         */
         sessionPlugins: mobx_state_tree_1.types.array(mobx_state_tree_1.types.frozen()),
     })
-        .volatile(( /* self */) => ({
-        /**
-         * #volatile
-         */
+        .volatile(() => ({
         sessionThemeName: (0, util_1.localStorageGetItem)('themeName') || 'default',
-        /**
-         * #volatile
-         * this is the current "task" that is being performed in the UI.
-         * this is usually an object of the form
-         * `{ taskName: "configure", target: thing_being_configured }`
-         */
         task: undefined,
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get tracks() {
             return [...self.sessionTracks, ...self.jbrowse.tracks];
         },
-        /**
-         * #getter
-         */
         get root() {
             return (0, mobx_state_tree_1.getParent)(self);
         },
-        /**
-         * #getter
-         * list of sessionAssemblies and jbrowse config assemblies, does not
-         * include temporaryAssemblies. basically the list to be displayed in a
-         * AssemblySelector dropdown
-         */
         get assemblies() {
             return [...self.jbrowse.assemblies, ...self.sessionAssemblies];
         },
-        /**
-         * #getter
-         * list of config connections and session connections
-         */
         get connections() {
             return [...self.jbrowse.connections, ...self.sessionConnections];
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setName(str) {
             self.name = str;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         * list of sessionAssemblies and jbrowse config assemblies, does not
-         * include temporaryAssemblies. basically the list to be displayed in a
-         * AssemblySelector dropdown
-         */
         get assemblyNames() {
             return self.assemblies.map(f => (0, configuration_1.readConfObject)(f, 'name'));
         },
-        /**
-         * #getter
-         */
         get version() {
             return self.root.version;
         },
-        /**
-         * #getter
-         */
         get shareURL() {
             return (0, configuration_1.getConf)(self.jbrowse, 'shareURL');
         },
-        /**
-         * #getter
-         */
         get textSearchManager() {
             return self.root.textSearchManager;
         },
-        /**
-         * #getter
-         */
         get assemblyManager() {
             return self.root.assemblyManager;
         },
-        /**
-         * #getter
-         */
-        get savedSessions() {
-            return self.root.savedSessions;
+        get savedSessionMetadata() {
+            return self.root.savedSessionMetadata;
         },
-        /**
-         * #getter
-         */
         get previousAutosaveId() {
             return self.root.previousAutosaveId;
         },
-        /**
-         * #getter
-         */
-        get savedSessionNames() {
-            return self.root.savedSessionNames;
-        },
-        /**
-         * #getter
-         */
         get history() {
             return self.root.history;
         },
-        /**
-         * #getter
-         */
-        get menus() {
-            return self.root.menus;
-        },
-        /**
-         * #method
-         */
         renderProps() {
             return {
                 theme: self.theme,
@@ -199,15 +114,9 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         addAssemblyConf(conf) {
             self.jbrowse.addAssemblyConf(conf);
         },
-        /**
-         * #action
-         */
         addSessionPlugin(plugin) {
             if (self.sessionPlugins.some(p => p.name === plugin.name)) {
                 throw new Error('session plugin cannot be installed twice');
@@ -215,80 +124,48 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
             self.sessionPlugins.push(plugin);
             self.root.setPluginsUpdated(true);
         },
-        /**
-         * #action
-         */
         removeSessionPlugin(pluginDefinition) {
-            self.sessionPlugins = (0, mobx_state_tree_1.cast)(self.sessionPlugins.filter(plugin => 
-            // @ts-expect-error
-            plugin.url !== pluginDefinition.url ||
-                // @ts-expect-error
+            self.sessionPlugins = (0, mobx_state_tree_1.cast)(self.sessionPlugins.filter(plugin => plugin.url !== pluginDefinition.url ||
                 plugin.umdUrl !== pluginDefinition.umdUrl ||
-                // @ts-expect-error
                 plugin.cjsUrl !== pluginDefinition.cjsUrl ||
-                // @ts-expect-error
                 plugin.esmUrl !== pluginDefinition.esmUrl));
             (0, mobx_state_tree_1.getParent)(self).setPluginsUpdated(true);
         },
-        /**
-         * #action
-         */
         addSavedSession(sessionSnapshot) {
             return self.root.addSavedSession(sessionSnapshot);
         },
-        /**
-         * #action
-         */
-        removeSavedSession(sessionSnapshot) {
-            return self.root.removeSavedSession(sessionSnapshot);
+        deleteSavedSession(id) {
+            return self.root.deleteSavedSession(id);
+        },
+        favoriteSavedSession(id) {
+            return self.root.favoriteSavedSession(id);
+        },
+        unfavoriteSavedSession(id) {
+            return self.root.unfavoriteSavedSession(id);
         },
-        /**
-         * #action
-         */
         renameCurrentSession(sessionName) {
             return self.root.renameCurrentSession(sessionName);
         },
-        /**
-         * #action
-         */
         duplicateCurrentSession() {
             return self.root.duplicateCurrentSession();
         },
-        /**
-         * #action
-         */
         activateSession(sessionName) {
             return self.root.activateSession(sessionName);
         },
-        /**
-         * #action
-         */
         setDefaultSession() {
             return self.root.setDefaultSession();
         },
-        /**
-         * #action
-         */
         saveSessionToLocalStorage() {
             return self.root.saveSessionToLocalStorage();
         },
-        /**
-         * #action
-         */
         loadAutosaveSession() {
             return self.root.loadAutosaveSession();
         },
-        /**
-         * #action
-         */
         setSession(sessionSnapshot) {
             return self.root.setSession(sessionSnapshot);
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         editTrackConfiguration(configuration) {
             const { adminMode, sessionTracks } = self;
             if (!adminMode && !sessionTracks.includes(configuration)) {
@@ -298,13 +175,9 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
         },
     }))
         .views(self => ({
-        /**
-         * #method
-         */
         getTrackActionMenuItems(config) {
             const { adminMode, sessionTracks } = self;
             const canEdit = adminMode || sessionTracks.find(t => t.trackId === config.trackId);
-            // disable if it is a reference sequence track
             const isRefSeq = config.type === 'ReferenceSequenceTrack';
             return [
                 {
@@ -313,7 +186,10 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                     onClick: () => {
                         self.queueDialog(handleClose => [
                             AboutDialog,
-                            { config, handleClose },
+                            {
+                                config,
+                                handleClose,
+                            },
                         ]);
                     },
                     icon: Info_1.default,
@@ -322,32 +198,31 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                     label: 'Settings',
                     priority: 1001,
                     disabled: !canEdit,
+                    icon: Settings_1.default,
                     onClick: () => {
                         self.editTrackConfiguration(config);
                     },
-                    icon: Settings_1.default,
                 },
                 {
                     label: 'Delete track',
                     priority: 1000,
                     disabled: !canEdit || isRefSeq,
-                    onClick: () => self.deleteTrackConf(config),
                     icon: Delete_1.default,
+                    onClick: () => {
+                        self.deleteTrackConf(config);
+                    },
                 },
                 {
                     label: 'Copy track',
                     priority: 999,
                     disabled: isRefSeq,
                     onClick: () => {
-                        const snap = (0, clone_1.default)((0, mobx_state_tree_1.getSnapshot)(config));
+                        const snap = structuredClone((0, mobx_state_tree_1.getSnapshot)(config));
                         const now = Date.now();
                         snap.trackId += `-${now}`;
                         snap.displays.forEach(display => {
                             display.displayId += `-${now}`;
                         });
-                        // the -sessionTrack suffix to trackId is used as metadata for
-                        // the track selector to store the track in a special category,
-                        // and default category is also cleared
                         if (!self.adminMode) {
                             snap.trackId += '-sessionTrack';
                             snap.category = undefined;
@@ -357,8 +232,12 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                     },
                     icon: FileCopy_1.default,
                 },
+                { type: 'divider' },
             ];
         },
+        menus() {
+            return self.root.menus();
+        },
     }))
         .actions(self => ({
         afterAttach() {
@@ -370,14 +249,8 @@ function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
     }));
     const extendedSessionModel = pluginManager.evaluateExtensionPoint('Core-extendSession', sessionModel);
     return mobx_state_tree_1.types.snapshotProcessor(extendedSessionModel, {
-        // @ts-expect-error
         preProcessor(snapshot) {
-            // @ts-expect-error
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             const { connectionInstances, ...rest } = snapshot || {};
-            // connectionInstances schema changed from object to an array, so any
-            // old connectionInstances as object is in snapshot, filter it out
-            // https://github.com/GMOD/jbrowse-components/issues/1903
             return !Array.isArray(connectionInstances) ? rest : snapshot;
         },
     });

package/dist/SessionConnections.d.ts

@@ -1,10 +1,6 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
-/**
- * #stateModel WebSessionConnectionsMixin
- * #category session
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { BaseConnectionConfigModel } from '@jbrowse/core/pluggableElementTypes/models/baseConnectionConfig';
 export declare function WebSessionConnectionsMixin(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     connectionInstances: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
         name: import("mobx-state-tree").ISimpleType<string>;
@@ -51,33 +47,9 @@ export declare function WebSessionConnectionsMixin(pluginManager: PluginManager)
         clear(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
 } & {
-    /**
-     * #property
-     */
     sessionConnections: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
 }, {
-    readonly connections: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-        name: {
-            type: string;
-            defaultValue: string;
-            description: string;
-        };
-        assemblyNames: {
-            type: string;
-            defaultValue: never[];
-            description: string;
-        };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>>)[];
+    readonly connections: BaseConnectionConfigModel[];
 } & {
     makeConnection(configuration: AnyConfigurationModel, initialSnapshot?: {}): ({
         name: string;
@@ -183,5 +155,5 @@ export declare function WebSessionConnectionsMixin(pluginManager: PluginManager)
     clearConnections(): void;
 } & {
     addConnectionConf(connectionConf: BaseConnectionConfigModel): any;
-    deleteConnection(configuration: AnyConfigurationModel): {} | undefined;
+    deleteConnection(configuration: AnyConfigurationModel): any;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/SessionConnections.js

@@ -1,18 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.WebSessionConnectionsMixin = WebSessionConnectionsMixin;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const product_core_1 = require("@jbrowse/product-core");
-/**
- * #stateModel WebSessionConnectionsMixin
- * #category session
- */
+const mobx_state_tree_1 = require("mobx-state-tree");
 function WebSessionConnectionsMixin(pluginManager) {
     return mobx_state_tree_1.types
         .compose('SessionConnectionsManagement', (0, product_core_1.ConnectionManagementSessionMixin)(pluginManager), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         sessionConnections: mobx_state_tree_1.types.array(pluginManager.pluggableConfigSchemaType('connection')),
     }))
         .actions(s => {
@@ -24,31 +17,32 @@ function WebSessionConnectionsMixin(pluginManager) {
                 if (self.adminMode) {
                     return superAddConnectionConf(connectionConf);
                 }
-                const { connectionId, type } = connectionConf;
-                if (!type) {
-                    throw new Error(`unknown connection type ${type}`);
-                }
-                const connection = self.sessionTracks.find(c => c.connectionId === connectionId);
-                if (connection) {
-                    return connection;
+                else {
+                    const { connectionId, type } = connectionConf;
+                    if (!type) {
+                        throw new Error(`unknown connection type ${type}`);
+                    }
+                    const connection = self.sessionTracks.find(c => c.connectionId === connectionId);
+                    if (connection) {
+                        return connection;
+                    }
+                    else {
+                        const length = self.sessionConnections.push(connectionConf);
+                        return self.sessionConnections[length - 1];
+                    }
                 }
-                const length = self.sessionConnections.push(connectionConf);
-                return self.sessionConnections[length - 1];
             },
             deleteConnection(configuration) {
-                let deletedConn;
                 if (self.adminMode) {
-                    deletedConn = superDeleteConnection(configuration);
+                    return superDeleteConnection(configuration);
                 }
-                if (!deletedConn) {
+                else {
                     const { connectionId } = configuration;
                     const idx = self.sessionConnections.findIndex(c => c.connectionId === connectionId);
-                    if (idx === -1) {
-                        return undefined;
-                    }
-                    return self.sessionConnections.splice(idx, 1);
+                    return idx === -1
+                        ? undefined
+                        : self.sessionConnections.splice(idx, 1);
                 }
-                return deletedConn;
             },
         };
     });