@jbrowse/product-core 5.0.0-beta.11 → 5.0.0-beta.14

package/esm/RootModel/createConfigModel.d.ts

@@ -69,11 +69,6 @@ declare function rootConfigurationSchema(): import("@jbrowse/core/configuration/
         } & {
             defaultValue: boolean;
         };
-        readonly useWorkspaces: {
-            type: "boolean";
-        } & {
-            defaultValue: boolean;
-        };
         readonly developerMode: {
             type: "boolean";
         } & {
@@ -191,11 +186,6 @@ export declare function createConfigModel(pluginManager: PluginManager, assembly
             } & {
                 defaultValue: boolean;
             };
-            readonly useWorkspaces: {
-                type: "boolean";
-            } & {
-                defaultValue: boolean;
-            };
             readonly developerMode: {
                 type: "boolean";
             } & {

package/esm/RootModel/index.d.ts

@@ -7,4 +7,4 @@ export { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.ts';
 export { PreferencesConfigSchemaFactory } from './PreferencesConfig.ts';
 export { createConfigModel } from './createConfigModel.ts';
 export type { RootConfigurationSnapshot } from './createConfigModel.ts';
-export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './menuItems.ts';
+export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './menuItems.ts';

package/esm/RootModel/index.js

@@ -7,4 +7,4 @@ export { FormatAboutConfigSchemaFactory, FormatDetailsConfigSchemaFactory, } fro
 export { HierarchicalConfigSchemaFactory } from './HierarchicalConfig.js';
 export { PreferencesConfigSchemaFactory } from './PreferencesConfig.js';
 export { createConfigModel } from './createConfigModel.js';
-export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, workspacesMenuItem, } from './menuItems.js';
+export { exportSessionMenuItem, importSessionMenuItem, newSessionMenuItem, openConnectionMenuItem, openTrackMenuItem, pluginStoreMenuItem, preferencesMenuItem, redoMenuItem, undoMenuItem, } from './menuItems.js';

package/esm/RootModel/menuItems.d.ts

@@ -1,7 +1,5 @@
-import type { SessionWithMultipleViews } from '../Session/index.ts';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { MenuItem } from '@jbrowse/core/ui';
-import type { DialogComponentType } from '@jbrowse/core/util';
 interface RootWithDefaultSession {
     setDefaultSession: () => void;
 }
@@ -11,7 +9,7 @@ export declare function exportSessionMenuItem(): MenuItem;
 export declare function openTrackMenuItem(): MenuItem;
 export declare function openConnectionMenuItem(): MenuItem;
 export declare function pluginStoreMenuItem(): MenuItem;
-export declare function preferencesMenuItem(pluginManager: PluginManager, PreferencesDialog: DialogComponentType): MenuItem;
+export declare function preferencesMenuItem(pluginManager: PluginManager): MenuItem;
 interface HistoryManager {
     canUndo: boolean;
     canRedo: boolean;
@@ -20,5 +18,4 @@ interface HistoryManager {
 }
 export declare function undoMenuItem(history: HistoryManager): MenuItem;
 export declare function redoMenuItem(history: HistoryManager): MenuItem;
-export declare function workspacesMenuItem(session: SessionWithMultipleViews | undefined): MenuItem;
 export {};

package/esm/RootModel/menuItems.js

@@ -1,3 +1,4 @@
+import { lazy } from 'react';
 import { Cable } from '@jbrowse/core/ui/Icons';
 import AddIcon from '@mui/icons-material/Add';
 import ExtensionIcon from '@mui/icons-material/Extension';
@@ -5,14 +6,13 @@ import GetAppIcon from '@mui/icons-material/GetApp';
 import PublishIcon from '@mui/icons-material/Publish';
 import RedoIcon from '@mui/icons-material/Redo';
 import SettingsIcon from '@mui/icons-material/Settings';
-import SpaceDashboardIcon from '@mui/icons-material/SpaceDashboard';
 import StorageIcon from '@mui/icons-material/Storage';
 import UndoIcon from '@mui/icons-material/Undo';
 import { getShareableSessionSnapshot } from '../Session/index.js';
+const PreferencesDialog = lazy(() => import('../ui/PreferencesDialog.js'));
 // the renderer binds the active session into each onClick (see AppToolbar's
 // wrapMenuItems), so these handlers receive it as their argument
 const MULTI_VIEW_WARNING = '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';
-const WORKSPACES_HELP_TEXT = 'Workspaces allow you to organize views into tabs and tiles. There are a variety of unique features, for instance, you can drag views between tabs or split them side-by-side. Try clicking and dragging the tab header to create a new split';
 export function newSessionMenuItem(root) {
     return {
         label: 'New session',
@@ -86,10 +86,7 @@ export function pluginStoreMenuItem() {
         },
     };
 }
-// the dialog component differs per product, so it is passed in rather than
-// imported; typing it as DialogComponentType lets queueDialog accept it with no
-// cast (the inline call sites needed `as BaseSession` to reach queueDialog)
-export function preferencesMenuItem(pluginManager, PreferencesDialog) {
+export function preferencesMenuItem(pluginManager) {
     return {
         label: 'Preferences',
         icon: SettingsIcon,
@@ -123,19 +120,3 @@ export function redoMenuItem(history) {
         },
     };
 }
-export function workspacesMenuItem(session) {
-    return {
-        label: 'Use workspaces',
-        icon: SpaceDashboardIcon,
-        type: 'checkbox',
-        checked: session?.effectiveUseWorkspaces ?? false,
-        helpText: WORKSPACES_HELP_TEXT,
-        // opts out of the checkbox "stay open" default: this re-lays out the whole
-        // app (classic stack <-> tiled workspace), so it's a one-shot mode switch
-        // rather than a setting to flip repeatedly with the menu up
-        keepMenuOpen: false,
-        onClick: () => {
-            session?.setUseWorkspacesPreference(!session.effectiveUseWorkspaces);
-        },
-    };
-}

package/esm/Session/BaseSession.d.ts

@@ -6,12 +6,12 @@ import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { AnimationMode, DialogComponentType, TrackConfigChange } from '@jbrowse/core/util';
 import type { HighlightType } from '@jbrowse/core/util/highlights';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
-type DoneCallback = (doneCallback: () => void) => [DialogComponentType, Record<string, unknown>];
+import type React from 'react';
 /**
  * #stateModel BaseSessionModel
  *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
+ * Holds a session's name, focused view, highlights and notifications. Every
+ * product's session composes this model, so add to it with care.
  */
 export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelType, JB_CONFIG_SCHEMA extends AnyConfigurationSchemaType>(_pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<Omit<{
     /**
@@ -139,10 +139,7 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     /**
      * #method
      * the admin/embedder `configuration.preferences` value for a key, ignoring
-     * any runtime override — i.e. what a reset falls back to. Exposed rather
-     * than inlined because "differs from the default" is a question the
-     * Preferences reset diff asks about settings this map doesn't hold (see
-     * `defaultUseWorkspaces`).
+     * any runtime override — i.e. what a reset falls back to
      */
     getPreferenceDefault(key: string): unknown;
     /**
@@ -273,12 +270,15 @@ export declare function BaseSessionModel<ROOT_MODEL_TYPE extends BaseRootModelTy
     setFocusedViewId(viewId: string | undefined): void;
     /**
      * #action
+     * Dismiss the dialog on screen as its own close button would, so a
+     * dialog that settles a promise on close (an internet account's token
+     * prompt) settles it, and drop it from the queue if it did not.
      */
     removeActiveDialog(): void;
     /**
      * #action
      */
-    queueDialog(doneCallback: DoneCallback): void;
+    queueDialog<T extends DialogComponentType>(callback: (doneCallback: () => void) => [T, React.ComponentProps<T>]): void;
     /**
      * #action
      */
@@ -306,4 +306,3 @@ export type BaseSession = Instance<BaseSessionType>;
 export declare function isBaseSession(thing: IAnyStateTreeNode): thing is BaseSession;
 /** Type guard for whether a thing is JBrowse session */
 export declare function isSession(thing: unknown): thing is BaseSession;
-export {};

package/esm/Session/BaseSession.js

@@ -14,8 +14,8 @@ function isAnimationMode(val) {
 /**
  * #stateModel BaseSessionModel
  *
- * base session shared by all JBrowse products. Be careful what you include
- * here, everything will use it.
+ * Holds a session's name, focused view, highlights and notifications. Every
+ * product's session composes this model, so add to it with care.
  */
 export function BaseSessionModel(_pluginManager) {
     const baseModel = types
@@ -172,10 +172,7 @@ export function BaseSessionModel(_pluginManager) {
         /**
          * #method
          * the admin/embedder `configuration.preferences` value for a key, ignoring
-         * any runtime override — i.e. what a reset falls back to. Exposed rather
-         * than inlined because "differs from the default" is a question the
-         * Preferences reset diff asks about settings this map doesn't hold (see
-         * `defaultUseWorkspaces`).
+         * any runtime override — i.e. what a reset falls back to
          */
         getPreferenceDefault(key) {
             const { preferences } = self.configuration;
@@ -393,17 +390,27 @@ export function BaseSessionModel(_pluginManager) {
         },
         /**
          * #action
+         * Dismiss the dialog on screen as its own close button would, so a
+         * dialog that settles a promise on close (an internet account's token
+         * prompt) settles it, and drop it from the queue if it did not.
          */
         removeActiveDialog() {
-            self.queueOfDialogs = self.queueOfDialogs.slice(1);
+            const active = self.queueOfDialogs[0];
+            const close = active?.[1].handleClose;
+            if (typeof close === 'function') {
+                close();
+            }
+            if (self.queueOfDialogs[0] === active) {
+                self.queueOfDialogs = self.queueOfDialogs.slice(1);
+            }
         },
         /**
          * #action
          */
-        queueDialog(doneCallback) {
+        queueDialog(callback) {
             // its own entry, not the head: a late second call must not close the
             // dialog queued behind it
-            const entry = doneCallback(() => {
+            const entry = callback(() => {
                 this.removeDialog(entry);
             });
             self.queueOfDialogs = [...self.queueOfDialogs, entry];

package/esm/Session/Connections.d.ts

@@ -13,6 +13,9 @@ export interface ConnectionTrackConfigEntry {
 }
 /**
  * #stateModel ConnectionManagementSessionMixin
+ * Adds connections to a session: the connection instances it has made, and
+ * the configs of the connection tracks the user opened, so those tracks load
+ * on session restore without reconnecting.
  */
 export declare function ConnectionManagementSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
     /**

package/esm/Session/Connections.js

@@ -3,6 +3,9 @@ import { asSession } from '../siblingCast.js';
 import { isBaseSession } from './BaseSession.js';
 /**
  * #stateModel ConnectionManagementSessionMixin
+ * Adds connections to a session: the connection instances it has made, and
+ * the configs of the connection tracks the user opened, so those tracks load
+ * on session restore without reconnecting.
  */
 export function ConnectionManagementSessionMixin(pluginManager) {
     return types

package/esm/Session/DrawerWidgets.d.ts

@@ -4,6 +4,8 @@ import type { DrawerPosition, Widget } from '@jbrowse/core/util/types';
 import type { IAnyStateTreeNode, Instance } from '@jbrowse/mobx-state-tree';
 /**
  * #stateModel DrawerWidgetSessionMixin
+ * Adds the widget drawer to a session: the open widgets, which one is
+ * showing, and the drawer's side, width and minimized state.
  */
 export declare function DrawerWidgetSessionMixin(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
     /**

package/esm/Session/DrawerWidgets.js

@@ -1,6 +1,7 @@
 import { isConfigurationModel } from '@jbrowse/core/configuration';
 import { localStorageGetItem, localStorageSetItem, scheduleDetachedDestroy, } from '@jbrowse/core/util';
-import { addDisposer, detach, getEnv, isAlive, isStateTreeNode, types, } from '@jbrowse/mobx-state-tree';
+import { getEditableTrackConfigById } from '@jbrowse/core/util/types';
+import { addDisposer, detach, getEnv, isAlive, types, } from '@jbrowse/mobx-state-tree';
 import { autorun } from 'mobx';
 import { isBaseSession } from './BaseSession.js';
 const minDrawerWidth = 128;
@@ -35,6 +36,8 @@ function clampDrawerWidth(width, availableWidth) {
 }
 /**
  * #stateModel DrawerWidgetSessionMixin
+ * Adds the widget drawer to a session: the open widgets, which one is
+ * showing, and the drawer's side, width and minimized state.
  */
 export function DrawerWidgetSessionMixin(pluginManager) {
     const widgetStateModelType = pluginManager.pluggableMstType('widget', 'stateModel');
@@ -264,23 +267,31 @@ export function DrawerWidgetSessionMixin(pluginManager) {
          * @param configuration - can be an MST model or a frozen/plain object with trackId
          */
         editConfiguration(configuration, opts) {
-            let targetConfig;
-            if (isStateTreeNode(configuration) &&
-                isConfigurationModel(configuration)) {
-                // Already an MST model (e.g., from track.configuration), use directly
-                targetConfig = configuration;
+            const isNode = isConfigurationModel(configuration);
+            if (!isNode && !('trackId' in configuration)) {
+                throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
             }
-            else if ('trackId' in configuration) {
-                // Frozen/plain object - create a temporary MST model for editing
-                const trackSchema = pluginManager.pluggableConfigSchemaType('track');
-                targetConfig = trackSchema.create(configuration, getEnv(self));
+            const trackId = configuration.trackId;
+            const workingCopy = typeof trackId === 'string'
+                ? getEditableTrackConfigById(self, trackId)
+                : undefined;
+            const editor = self.openWidget('ConfigurationEditorWidget', 'configEditor');
+            // A shown track edits its working copy, so the editor edits that same
+            // node, and follows it when an undo replaces it (ADR-032). A node the
+            // session does not resolve by id, such as a track a view holds
+            // inline, is edited as it stands.
+            if (typeof trackId === 'string' &&
+                workingCopy &&
+                (!isNode || workingCopy === configuration)) {
+                editor.setTrackId(trackId);
             }
             else {
-                throw new Error('must pass a configuration model or frozen config with trackId to editConfiguration');
+                editor.setTarget(isNode
+                    ? configuration
+                    : pluginManager
+                        .pluggableConfigSchemaType('track')
+                        .create(configuration, getEnv(self)));
             }
-            const editor = self.openWidget('ConfigurationEditorWidget', 'configEditor');
-            // Set target via action since it's now volatile
-            editor.setTarget(targetConfig);
             editor.setExpandedDisplayId(opts?.expandedDisplayId);
         },
     }))