@jbrowse/web-core 2.17.0 → 2.18.0

package/esm/BaseWebSession/index.js

@@ -1,167 +1,72 @@
 import { lazy } from 'react';
-import clone from 'clone';
-import { getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
-import { autorun } from 'mobx';
-import { addDisposer, cast, getParent, getSnapshot, types, } from 'mobx-state-tree';
-import { DialogQueueSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, } from '@jbrowse/product-core';
 import { AppFocusMixin, SessionAssembliesMixin, TemporaryAssembliesMixin, } from '@jbrowse/app-core';
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
 import SnackbarModel from '@jbrowse/core/ui/SnackbarModel';
-// icons
-import SettingsIcon from '@mui/icons-material/Settings';
-import CopyIcon from '@mui/icons-material/FileCopy';
+import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util';
+import { DialogQueueSessionMixin, DrawerWidgetSessionMixin, MultipleViewsSessionMixin, ReferenceManagementSessionMixin, SessionTracksManagerSessionMixin, ThemeManagerSessionMixin, } from '@jbrowse/product-core';
 import DeleteIcon from '@mui/icons-material/Delete';
+import CopyIcon from '@mui/icons-material/FileCopy';
 import InfoIcon from '@mui/icons-material/Info';
-// locals
+import SettingsIcon from '@mui/icons-material/Settings';
+import { autorun } from 'mobx';
+import { addDisposer, cast, getParent, getSnapshot, types, } from 'mobx-state-tree';
 import { WebSessionConnectionsMixin } from '../SessionConnections';
-// lazies
 const AboutDialog = lazy(() => import('./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)
- */
 export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
     const sessionModel = types
         .compose('WebCoreSessionModel', types.compose('WebCoreSessionModelGroupA', ReferenceManagementSessionMixin(pluginManager), DrawerWidgetSessionMixin(pluginManager), DialogQueueSessionMixin(pluginManager), ThemeManagerSessionMixin(pluginManager), MultipleViewsSessionMixin(pluginManager)), types.compose('WebCoreSessionModelGroupB', SessionTracksManagerSessionMixin(pluginManager), SessionAssembliesMixin(pluginManager, assemblyConfigSchema), TemporaryAssembliesMixin(pluginManager, assemblyConfigSchema), WebSessionConnectionsMixin(pluginManager), AppFocusMixin(), SnackbarModel()))
         .props({
-        /**
-         * #property
-         */
         margin: 0,
-        /**
-         * #property
-         */
         sessionPlugins: types.array(types.frozen()),
     })
-        .volatile(( /* self */) => ({
-        /**
-         * #volatile
-         */
+        .volatile(() => ({
         sessionThemeName: 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 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 => readConfObject(f, 'name'));
         },
-        /**
-         * #getter
-         */
         get version() {
             return self.root.version;
         },
-        /**
-         * #getter
-         */
         get shareURL() {
             return 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,
@@ -170,15 +75,9 @@ export 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');
@@ -186,80 +85,48 @@ export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
             self.sessionPlugins.push(plugin);
             self.root.setPluginsUpdated(true);
         },
-        /**
-         * #action
-         */
         removeSessionPlugin(pluginDefinition) {
-            self.sessionPlugins = cast(self.sessionPlugins.filter(plugin => 
-            // @ts-expect-error
-            plugin.url !== pluginDefinition.url ||
-                // @ts-expect-error
+            self.sessionPlugins = 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));
             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)) {
@@ -269,13 +136,9 @@ export 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 [
                 {
@@ -284,7 +147,10 @@ export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                     onClick: () => {
                         self.queueDialog(handleClose => [
                             AboutDialog,
-                            { config, handleClose },
+                            {
+                                config,
+                                handleClose,
+                            },
                         ]);
                     },
                     icon: InfoIcon,
@@ -293,32 +159,31 @@ export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                     label: 'Settings',
                     priority: 1001,
                     disabled: !canEdit,
+                    icon: SettingsIcon,
                     onClick: () => {
                         self.editTrackConfiguration(config);
                     },
-                    icon: SettingsIcon,
                 },
                 {
                     label: 'Delete track',
                     priority: 1000,
                     disabled: !canEdit || isRefSeq,
-                    onClick: () => self.deleteTrackConf(config),
                     icon: DeleteIcon,
+                    onClick: () => {
+                        self.deleteTrackConf(config);
+                    },
                 },
                 {
                     label: 'Copy track',
                     priority: 999,
                     disabled: isRefSeq,
                     onClick: () => {
-                        const snap = clone(getSnapshot(config));
+                        const snap = structuredClone(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;
@@ -330,6 +195,9 @@ export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
                 },
             ];
         },
+        menus() {
+            return self.root.menus();
+        },
     }))
         .actions(self => ({
         afterAttach() {
@@ -341,14 +209,8 @@ export function BaseWebSession({ pluginManager, assemblyConfigSchema, }) {
     }));
     const extendedSessionModel = pluginManager.evaluateExtensionPoint('Core-extendSession', sessionModel);
     return 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/esm/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>;
@@ -51,9 +47,6 @@ 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: ({

package/esm/SessionConnections.js

@@ -1,15 +1,8 @@
+import { ConnectionManagementSessionMixin } from '@jbrowse/product-core';
 import { types } from 'mobx-state-tree';
-import { ConnectionManagementSessionMixin, } from '@jbrowse/product-core';
-/**
- * #stateModel WebSessionConnectionsMixin
- * #category session
- */
 export function WebSessionConnectionsMixin(pluginManager) {
     return types
         .compose('SessionConnectionsManagement', ConnectionManagementSessionMixin(pluginManager), types.model({
-        /**
-         * #property
-         */
         sessionConnections: types.array(pluginManager.pluggableConfigSchemaType('connection')),
     }))
         .actions(s => {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/web-core",
-  "version": "2.17.0",
+  "version": "2.18.0",
   "description": "JBrowse 2 code shared between web-app type products",
   "keywords": [
     "jbrowse",
@@ -42,11 +42,10 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/app-core": "^2.17.0",
-    "@jbrowse/product-core": "^2.17.0",
+    "@jbrowse/app-core": "^2.18.0",
+    "@jbrowse/product-core": "^2.18.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
-    "clone": "^2.0.0",
     "copy-to-clipboard": "^3.3.1"
   },
   "peerDependencies": {
@@ -61,5 +60,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }