@jbrowse/plugin-data-management 2.11.0 → 2.11.2

package/dist/AddConnectionWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function AddConnectionWidgetF(pluginManager: PluginManager): void;

package/dist/AddConnectionWidget/index.js

@@ -31,7 +31,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('AddConnectionWidget', {});
-exports.default = (pluginManager) => {
+function AddConnectionWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new pluggableElementTypes_1.WidgetType({
             name: 'AddConnectionWidget',
@@ -41,4 +41,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddConnectionWidget')))),
         });
     });
-};
+}
+exports.default = AddConnectionWidgetF;

package/dist/AddTrackWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function AddTrackWidgetF(pluginManager: PluginManager): void;

package/dist/AddTrackWidget/index.js

@@ -31,7 +31,7 @@ const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('AddTrackWidget', {});
-exports.default = (pluginManager) => {
+function AddTrackWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new pluggableElementTypes_1.WidgetType({
             name: 'AddTrackWidget',
@@ -41,4 +41,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddTrackWidget')))),
         });
     });
-};
+}
+exports.default = AddTrackWidgetF;

package/dist/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.js

@@ -1,9 +1,32 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const react_1 = __importStar(require("react"));
 const mobx_1 = require("mobx");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
@@ -11,9 +34,7 @@ const x_data_grid_1 = require("@mui/x-data-grid");
 // jbrowse
 const ui_1 = require("@jbrowse/core/ui");
 const SanitizedHTML_1 = __importDefault(require("@jbrowse/core/ui/SanitizedHTML"));
-const ResizeBar_1 = __importDefault(require("@jbrowse/core/ui/ResizeBar"));
 const util_1 = require("@jbrowse/core/util");
-const useResizeBar_1 = require("@jbrowse/core/ui/useResizeBar");
 const mui_1 = require("tss-react/mui");
 const FacetedHeader_1 = __importDefault(require("./FacetedHeader"));
 const FacetFilters_1 = __importDefault(require("./FacetFilters"));
@@ -35,10 +56,25 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
     var _a;
     const { classes } = useStyles();
     const { view, selection, shownTrackIds, faceted } = model;
-    const { rows, panelWidth, showFilters, useShoppingCart, showOptions, filteredRows, filteredNonMetadataKeys, filteredMetadataKeys, visible, widths, } = faceted;
+    const { rows, panelWidth, showFilters, useShoppingCart, showOptions, filteredRows, filteredNonMetadataKeys, filteredMetadataKeys, visible, } = faceted;
     const { pluginManager } = (0, util_1.getEnv)(model);
-    const { ref, scrollLeft } = (0, useResizeBar_1.useResizeBar)();
-    const widthsDebounced = (0, util_1.useDebounce)(widths, 200);
+    const [widths, setWidths] = (0, react_1.useState)({
+        name: (0, util_1.measureGridWidth)(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
+        ...Object.fromEntries(filteredNonMetadataKeys
+            .filter(f => visible[f])
+            .map(e => [
+            e,
+            (0, util_1.measureGridWidth)(rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
+        ])),
+        ...Object.fromEntries(filteredMetadataKeys
+            .filter(f => visible['metadata.' + f])
+            .map(e => {
+            return [
+                'metadata.' + e,
+                (0, util_1.measureGridWidth)(rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
+            ];
+        })),
+    });
     const columns = [
         {
             field: 'name',
@@ -50,13 +86,13 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
                     react_1.default.createElement(SanitizedHTML_1.default, { html: value }),
                     react_1.default.createElement(TrackLabelMenu_1.default, { id: id, conf: conf, trackId: id, model: model })));
             },
-            width: (_a = widthsDebounced.name) !== null && _a !== void 0 ? _a : 100,
+            width: (_a = widths.name) !== null && _a !== void 0 ? _a : 100,
         },
         ...filteredNonMetadataKeys.map(e => {
             var _a;
             return {
                 field: e,
-                width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
+                width: (_a = widths[e]) !== null && _a !== void 0 ? _a : 100,
                 renderCell: params => {
                     const val = params.value;
                     return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
@@ -70,8 +106,8 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
                 headerName: ['name', ...filteredNonMetadataKeys].includes(e)
                     ? `${e} (from metadata)`
                     : e,
-                width: (_a = widthsDebounced['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
-                valueGetter: (_, row) => `${row.metadata[e]}`,
+                width: (_a = widths['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
+                valueGetter: (_, row) => { var _a; return `${(_a = row.metadata[e]) !== null && _a !== void 0 ? _a : ''}`; },
                 renderCell: params => {
                     const val = params.value;
                     return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
@@ -81,7 +117,7 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
     ];
     return (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(FacetedHeader_1.default, { model: model }),
-        react_1.default.createElement("div", { ref: ref, style: {
+        react_1.default.createElement("div", { style: {
                 display: 'flex',
                 overflow: 'hidden',
                 height: window.innerHeight * frac,
@@ -91,11 +127,7 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
                     height: window.innerHeight * frac,
                     width: window.innerWidth * frac - (showFilters ? panelWidth : 0),
                 } },
-                react_1.default.createElement(ResizeBar_1.default, { checkbox: true, widths: Object.values(widths).map(f => f !== null && f !== void 0 ? f : 100), setWidths: newWidths => faceted.setWidths(Object.fromEntries(Object.entries(widths).map((entry, idx) => [
-                        entry[0],
-                        newWidths[idx],
-                    ]))), scrollLeft: scrollLeft }),
-                react_1.default.createElement(x_data_grid_1.DataGrid, { rows: filteredRows, columnVisibilityModel: visible, onColumnVisibilityModelChange: n => faceted.setVisible(n), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
+                react_1.default.createElement(x_data_grid_1.DataGrid, { rows: filteredRows, onColumnWidthChange: arg => setWidths({ ...widths, [arg.colDef.field]: arg.width }), columnVisibilityModel: visible, onColumnVisibilityModelChange: n => faceted.setVisible(n), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
                         if (!useShoppingCart) {
                             const a1 = shownTrackIds;
                             const a2 = new Set(userSelectedIds);

package/dist/HierarchicalTrackSelectorWidget/facetedModel.d.ts

@@ -25,7 +25,6 @@ export declare function facetedStateTreeF(): import("mobx-state-tree").IModelTyp
     panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
 }, {
     visible: Record<string, boolean>;
-    widths: Record<string, number | undefined>;
     useShoppingCart: boolean;
     filters: import("mobx").ObservableMap<string, string[]>;
 } & {
@@ -118,10 +117,6 @@ export declare function facetedStateTreeF(): import("mobx-state-tree").IModelTyp
      * #action
      */
     setVisible(args: Record<string, boolean>): void;
-    /**
-     * #action
-     */
-    setWidths(args: Record<string, number | undefined>): void;
     afterAttach(): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type FacetedStateModel = ReturnType<typeof facetedStateTreeF>;

package/dist/HierarchicalTrackSelectorWidget/facetedModel.js

@@ -39,7 +39,6 @@ function facetedStateTreeF() {
     })
         .volatile(() => ({
         visible: {},
-        widths: {},
         useShoppingCart: false,
         filters: mobx_1.observable.map(),
     }))
@@ -167,35 +166,10 @@ function facetedStateTreeF() {
         setVisible(args) {
             self.visible = args;
         },
-        /**
-         * #action
-         */
-        setWidths(args) {
-            self.widths = args;
-        },
         afterAttach() {
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
                 this.setVisible(Object.fromEntries(self.fields.map(c => [c, true])));
             }));
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                this.setWidths({
-                    name: (0, util_2.measureGridWidth)(self.rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
-                    ...Object.fromEntries(self.filteredNonMetadataKeys
-                        .filter(f => self.visible[f])
-                        .map(e => [
-                        e,
-                        (0, util_2.measureGridWidth)(self.rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
-                    ])),
-                    ...Object.fromEntries(self.filteredMetadataKeys
-                        .filter(f => self.visible['metadata.' + f])
-                        .map(e => {
-                        return [
-                            'metadata.' + e,
-                            (0, util_2.measureGridWidth)(self.rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
-                        ];
-                    })),
-                });
-            }));
         },
     }));
 }

package/dist/HierarchicalTrackSelectorWidget/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HierarchicalTrackSelectorWidgetF(pluginManager: PluginManager): void;
 export { type HierarchicalTrackSelectorModel, default as stateModelFactory, } from './model';
 export { default as configSchema } from './configSchema';

package/dist/HierarchicalTrackSelectorWidget/index.js

@@ -31,7 +31,7 @@ const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const react_1 = require("react");
-exports.default = (pluginManager) => {
+function HierarchicalTrackSelectorWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new pluggableElementTypes_1.WidgetType({
             name: 'HierarchicalTrackSelectorWidget',
@@ -41,7 +41,8 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/HierarchicalTrackSelector')))),
         });
     });
-};
+}
+exports.default = HierarchicalTrackSelectorWidgetF;
 var model_2 = require("./model");
 Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
 var configSchema_2 = require("./configSchema");

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -14,22 +14,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #property
      */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
-    /**
-     * #property
-     */
-    initialized: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    sortTrackNames: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    sortCategories: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     /**
      * #property
      */
@@ -45,7 +29,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         visible: Record<string, boolean>;
-        widths: Record<string, number | undefined>;
         useShoppingCart: boolean;
         filters: import("mobx").ObservableMap<string, string[]>;
     } & {
@@ -54,7 +37,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         setUseShoppingCart(f: boolean): void;
         setFilterText(str: string): void;
         setShowSparse(f: boolean): void;
-        setShowOptions(f: boolean): void;
+        setShowOptions(f: boolean): void; /**
+         * #property
+         */
         setShowFilters(f: boolean): void;
     } & {
         readonly allTrackConfigurations: ({
@@ -96,7 +81,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         }[];
     } & {
         setVisible(args: Record<string, boolean>): void;
-        setWidths(args: Record<string, number | undefined>): void;
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
@@ -107,6 +91,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    sortTrackNames: boolean;
+    sortCategories: boolean;
+    collapsed: import("mobx").ObservableMap<string, boolean>;
     filterText: string;
     recentlyUsedCounter: number;
     favoritesCounter: number;
@@ -131,6 +118,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #getter
      */
     readonly recentlyUsedSet: Set<string>;
+    /**
+     * #getter
+     */
+    readonly assemblyNames: string[];
 } & {
     /**
      * #action
@@ -208,6 +199,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #action
      */
     expandAllCategories(): void;
+    /**
+     * #action
+     */
+    setCollapsedCategories(str: [string, boolean][]): void;
     /**
      * #action
      */
@@ -237,24 +232,11 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     /**
      * #getter
      */
-    readonly assemblyNames: string[];
-} & {
-    /**
-     * #getter
-     */
-    readonly recentlyUsedLocalStorageKey: string;
+    readonly activeSortTrackNames: boolean;
     /**
      * #getter
      */
-    readonly favoritesLocalStorageKey: string;
-    /**
-     * #getter
-     */
-    readonly activeSortTrackNames: any;
-    /**
-     * #getter
-     */
-    readonly activeSortCategories: any;
+    readonly activeSortCategories: boolean;
     /**
      * #getter
      * filter out tracks that don't match the current assembly/display types
@@ -340,8 +322,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #action
      */
     collapseTopLevelCategories(): void;
-} & {
-    afterCreate(): void;
 } & {
     /**
      * #getter

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -10,21 +10,52 @@ const filterTracks_1 = require("./filterTracks");
 const generateHierarchy_1 = require("./generateHierarchy");
 const util_2 = require("./util");
 const facetedModel_1 = require("./facetedModel");
-// for settings that are config dependent
-function postNoConfigF() {
+// for settings that are not config dependent
+function keyNoConfigPostFix() {
     return typeof window !== 'undefined'
         ? [window.location.host, window.location.pathname].join('-')
         : 'empty';
 }
-// for settings that are not config dependent
-function postF() {
+// for settings that are config dependent
+function keyConfigPostFix() {
     return typeof window !== 'undefined'
         ? [
-            postNoConfigF(),
+            keyNoConfigPostFix(),
             new URLSearchParams(window.location.search).get('config'),
         ].join('-')
         : 'empty';
 }
+function recentlyUsedK(assemblyNames) {
+    return ['recentlyUsedTracks', keyConfigPostFix(), assemblyNames.join(',')]
+        .filter(f => !!f)
+        .join('-');
+}
+// this has a extra } at the end because that's how it was initially
+// released
+function favoritesK() {
+    return `favoriteTracks-${keyConfigPostFix()}}`;
+}
+function collapsedK(assemblyNames, viewType) {
+    return [
+        'collapsedCategories',
+        keyConfigPostFix(),
+        assemblyNames.join(','),
+        viewType,
+    ].join('-');
+}
+function sortTrackNamesK() {
+    return 'sortTrackNames';
+}
+function sortCategoriesK() {
+    return 'sortCategories';
+}
+function localStorageGetJSON(key, defaultValue) {
+    var _a;
+    return JSON.parse((_a = (0, util_1.localStorageGetItem)(key)) !== null && _a !== void 0 ? _a : defaultValue);
+}
+function localStorageSetJSON(key, val) {
+    (0, util_1.localStorageSetItem)(key, JSON.stringify(val));
+}
 const MAX_RECENTLY_USED = 10;
 /**
  * #stateModel HierarchicalTrackSelectorWidget
@@ -40,22 +71,6 @@ function stateTreeFactory(pluginManager) {
          * #property
          */
         type: mobx_state_tree_1.types.literal('HierarchicalTrackSelectorWidget'),
-        /**
-         * #property
-         */
-        initialized: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        collapsed: mobx_state_tree_1.types.map(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        sortTrackNames: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        /**
-         * #property
-         */
-        sortCategories: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
         /**
          * #property
          */
@@ -66,9 +81,12 @@ function stateTreeFactory(pluginManager) {
         faceted: mobx_state_tree_1.types.optional((0, facetedModel_1.facetedStateTreeF)(), {}),
     })
         .volatile(() => ({
-        favorites: [],
+        favorites: localStorageGetJSON(favoritesK(), '[]'),
         recentlyUsed: [],
         selection: [],
+        sortTrackNames: !!localStorageGetJSON(sortTrackNamesK(), 'false'),
+        sortCategories: !!localStorageGetJSON(sortCategoriesK(), 'false'),
+        collapsed: mobx_1.observable.map(),
         filterText: '',
         recentlyUsedCounter: 0,
         favoritesCounter: 0,
@@ -99,6 +117,13 @@ function stateTreeFactory(pluginManager) {
         get recentlyUsedSet() {
             return new Set(self.recentlyUsed);
         },
+        /**
+         * #getter
+         */
+        get assemblyNames() {
+            var _a;
+            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        },
     }))
         .actions(self => ({
         /**
@@ -223,6 +248,12 @@ function stateTreeFactory(pluginManager) {
         expandAllCategories() {
             self.collapsed.clear();
         },
+        /**
+         * #action
+         */
+        setCollapsedCategories(str) {
+            self.collapsed.replace(str);
+        },
         /**
          * #action
          */
@@ -263,43 +294,17 @@ function stateTreeFactory(pluginManager) {
             const assembly = assemblyManager.get(assemblyName);
             const trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
             const viewType = pluginManager.getViewType(self.view.type);
-            if (!trackConf) {
-                return undefined;
-            }
-            for (const display of trackConf.displays) {
-                if (viewType.displayTypes.some(d => d.name === display.type)) {
-                    return trackConf;
+            if (trackConf) {
+                for (const display of trackConf.displays) {
+                    if (viewType.displayTypes.some(d => d.name === display.type)) {
+                        return trackConf;
+                    }
                 }
             }
             return undefined;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
-        get assemblyNames() {
-            var _a;
-            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
-        },
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get recentlyUsedLocalStorageKey() {
-            return `recentlyUsedTracks-${[postF(), self.assemblyNames.join(',')]
-                .filter(f => !!f)
-                .join('-')}`;
-        },
-        /**
-         * #getter
-         */
-        get favoritesLocalStorageKey() {
-            // this has a extra } at the end because that's how it was initially
-            // released
-            return `favoriteTracks-${postF()}}`;
-        },
         /**
          * #getter
          */
@@ -434,35 +439,6 @@ function stateTreeFactory(pluginManager) {
                 self.setCategoryCollapsed(path, true);
             }
         },
-    }))
-        .actions(self => ({
-        afterCreate() {
-            if (!self.initialized) {
-                const session = (0, util_1.getSession)(self);
-                if ((0, configuration_1.getConf)(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'topLevelCategories',
-                ])) {
-                    self.collapseTopLevelCategories();
-                }
-                if ((0, configuration_1.getConf)(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'subCategories',
-                ])) {
-                    self.collapseSubCategories();
-                }
-                for (const entry of (0, configuration_1.getConf)(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'categoryNames',
-                ])) {
-                    self.collapsed.set(entry, true);
-                }
-                self.initialized = true;
-            }
-        },
     }))
         .views(self => ({
         /**
@@ -476,13 +452,50 @@ function stateTreeFactory(pluginManager) {
         afterAttach() {
             // this should be the first autorun to properly initialize
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                self.setRecentlyUsed(JSON.parse((0, util_1.localStorageGetItem)(self.recentlyUsedLocalStorageKey) || '[]'));
-                self.setFavorites(JSON.parse((0, util_1.localStorageGetItem)(self.favoritesLocalStorageKey) || '[]'));
+                const { assemblyNames, view } = self;
+                self.setRecentlyUsed(localStorageGetJSON(recentlyUsedK(assemblyNames), '[]'));
+                if (view) {
+                    const val = (0, util_1.localStorageGetItem)(collapsedK(assemblyNames, view.type));
+                    if (!val) {
+                        self.expandAllCategories();
+                        const session = (0, util_1.getSession)(self);
+                        if ((0, configuration_1.getConf)(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'topLevelCategories',
+                        ])) {
+                            self.collapseTopLevelCategories();
+                        }
+                        if ((0, configuration_1.getConf)(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'subCategories',
+                        ])) {
+                            self.collapseSubCategories();
+                        }
+                        for (const entry of (0, configuration_1.getConf)(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'categoryNames',
+                        ])) {
+                            self.setCategoryCollapsed(`Tracks-${entry}`, true);
+                        }
+                    }
+                    else {
+                        self.setCollapsedCategories(JSON.parse(val));
+                    }
+                }
             }));
             // this should be the second autorun
             (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(() => {
-                (0, util_1.localStorageSetItem)(self.favoritesLocalStorageKey, JSON.stringify(self.favorites));
-                (0, util_1.localStorageSetItem)(self.recentlyUsedLocalStorageKey, JSON.stringify(self.recentlyUsed));
+                const { assemblyNames, collapsed, view } = self;
+                localStorageSetJSON(recentlyUsedK(assemblyNames), self.recentlyUsed);
+                localStorageSetJSON(favoritesK(), self.favorites);
+                localStorageSetJSON(sortTrackNamesK(), self.sortTrackNames);
+                localStorageSetJSON(sortCategoriesK(), self.sortCategories);
+                if (view) {
+                    localStorageSetJSON(collapsedK(assemblyNames, view.type), collapsed);
+                }
             }));
         },
     }));

package/dist/HierarchicalTrackSelectorWidget/util.d.ts

@@ -7,6 +7,6 @@ interface Node {
     children: Node[];
     id: string;
 }
-export declare function findSubCategories(obj: Node[], paths: string[]): boolean;
+export declare function findSubCategories(obj: Node[], paths: string[], depth?: number): boolean;
 export declare function findTopLevelCategories(obj: Node[], paths: string[]): void;
 export {};

package/dist/HierarchicalTrackSelectorWidget/util.js

@@ -27,12 +27,13 @@ function matches(query, conf, session) {
         !!categories.filter(c => c.toLowerCase().includes(queryLower)).length);
 }
 exports.matches = matches;
-function findSubCategories(obj, paths) {
+function findSubCategories(obj, paths, depth = 0) {
     let hasSubs = false;
     for (const elt of obj) {
         if (elt.children.length) {
-            const hasSubCategories = findSubCategories(elt.children, paths);
-            if (hasSubCategories) {
+            const hasSubCategories = findSubCategories(elt.children, paths, depth + 1);
+            // avoid pushing the root "Tracks" node by checking depth>0
+            if (hasSubCategories && depth > 0) {
                 paths.push(elt.id);
             }
         }

package/dist/PluginStoreWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function PluginStoreWidgetF(pluginManager: PluginManager): void;