@jbrowse/plugin-data-management 2.11.0 → 2.11.2

package/dist/PluginStoreWidget/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)('PluginStoreWidget', {});
-exports.default = (pluginManager) => {
+function PluginStoreWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new pluggableElementTypes_1.WidgetType({
             name: 'PluginStoreWidget',
@@ -41,4 +41,5 @@ exports.default = (pluginManager) => {
             ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/PluginStoreWidget')))),
         });
     });
-};
+}
+exports.default = PluginStoreWidgetF;

package/dist/index.d.ts

@@ -5,7 +5,7 @@ declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel,
     rootModel: any;
     onClose: (arg: boolean) => void;
 }) => import("react").JSX.Element>;
-export default class extends Plugin {
+export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
         AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {

package/dist/index.js

@@ -36,7 +36,7 @@ const PluginStoreWidget_1 = __importDefault(require("./PluginStoreWidget"));
 const HierarchicalTrackSelectorWidget_1 = __importDefault(require("./HierarchicalTrackSelectorWidget"));
 const AssemblyManager = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AssemblyManager'))));
 exports.AssemblyManager = AssemblyManager;
-class default_1 extends Plugin_1.default {
+class DataManagementPlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);
         this.name = 'DataManagementPlugin';
@@ -53,4 +53,4 @@ class default_1 extends Plugin_1.default {
     }
     configure(_pluginManager) { }
 }
-exports.default = default_1;
+exports.default = DataManagementPlugin;

package/dist/ucsc-trackhub/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 UCSCTrackHubConnectionF(pluginManager: PluginManager): void;

package/dist/ucsc-trackhub/index.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
-exports.default = (pluginManager) => {
+function UCSCTrackHubConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new pluggableElementTypes_1.ConnectionType({
         name: 'UCSCTrackHubConnection',
         configSchema: configSchema_1.default,
@@ -15,4 +15,5 @@ exports.default = (pluginManager) => {
         description: 'A track or assembly hub in the Track Hub format',
         url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
     }));
-};
+}
+exports.default = UCSCTrackHubConnectionF;

package/esm/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/esm/AddConnectionWidget/index.js

@@ -3,7 +3,7 @@ import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
 import { lazy } from 'react';
 import stateModel from './model';
 const configSchema = ConfigurationSchema('AddConnectionWidget', {});
-export default (pluginManager) => {
+export default function AddConnectionWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new WidgetType({
             name: 'AddConnectionWidget',
@@ -13,4 +13,4 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/AddConnectionWidget')),
         });
     });
-};
+}

package/esm/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/esm/AddTrackWidget/index.js

@@ -3,7 +3,7 @@ import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
 import { lazy } from 'react';
 import stateModelFactory from './model';
 const configSchema = ConfigurationSchema('AddTrackWidget', {});
-export default (pluginManager) => {
+export default function AddTrackWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new WidgetType({
             name: 'AddTrackWidget',
@@ -13,4 +13,4 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/AddTrackWidget')),
         });
     });
-};
+}

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

@@ -1,4 +1,4 @@
-import React from 'react';
+import React, { useState } from 'react';
 import { transaction } from 'mobx';
 import { observer } from 'mobx-react';
 import { getRoot, resolveIdentifier } from 'mobx-state-tree';
@@ -6,9 +6,7 @@ import { DataGrid, GridToolbar } from '@mui/x-data-grid';
 // jbrowse
 import { ResizeHandle } from '@jbrowse/core/ui';
 import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
-import ResizeBar from '@jbrowse/core/ui/ResizeBar';
-import { getEnv, useDebounce } from '@jbrowse/core/util';
-import { useResizeBar } from '@jbrowse/core/ui/useResizeBar';
+import { getEnv, measureGridWidth } from '@jbrowse/core/util';
 import { makeStyles } from 'tss-react/mui';
 import FacetedHeader from './FacetedHeader';
 import FacetFilters from './FacetFilters';
@@ -30,10 +28,25 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
     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 } = getEnv(model);
-    const { ref, scrollLeft } = useResizeBar();
-    const widthsDebounced = useDebounce(widths, 200);
+    const [widths, setWidths] = useState({
+        name: measureGridWidth(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
+        ...Object.fromEntries(filteredNonMetadataKeys
+            .filter(f => visible[f])
+            .map(e => [
+            e,
+            measureGridWidth(rows.map(r => r[e]), { maxWidth: 400, stripHTML: true }),
+        ])),
+        ...Object.fromEntries(filteredMetadataKeys
+            .filter(f => visible['metadata.' + f])
+            .map(e => {
+            return [
+                'metadata.' + e,
+                measureGridWidth(rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
+            ];
+        })),
+    });
     const columns = [
         {
             field: 'name',
@@ -45,13 +58,13 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
                     React.createElement(SanitizedHTML, { html: value }),
                     React.createElement(TrackLabelMenu, { 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.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
@@ -65,8 +78,8 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
                 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.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
@@ -76,7 +89,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
     ];
     return (React.createElement(React.Fragment, null,
         React.createElement(FacetedHeader, { model: model }),
-        React.createElement("div", { ref: ref, style: {
+        React.createElement("div", { style: {
                 display: 'flex',
                 overflow: 'hidden',
                 height: window.innerHeight * frac,
@@ -86,11 +99,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
                     height: window.innerHeight * frac,
                     width: window.innerWidth * frac - (showFilters ? panelWidth : 0),
                 } },
-                React.createElement(ResizeBar, { 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.createElement(DataGrid, { rows: filteredRows, columnVisibilityModel: visible, onColumnVisibilityModelChange: n => faceted.setVisible(n), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
+                React.createElement(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/esm/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/esm/HierarchicalTrackSelectorWidget/facetedModel.js

@@ -2,7 +2,7 @@ import { addDisposer, getParent, types } from 'mobx-state-tree';
 import { matches } from './util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { getTrackName } from '@jbrowse/core/util/tracks';
-import { getSession, localStorageGetItem, measureGridWidth, } from '@jbrowse/core/util';
+import { getSession, localStorageGetItem } from '@jbrowse/core/util';
 import { autorun, observable } from 'mobx';
 import { getRootKeys, findNonSparseKeys } from './facetedUtil';
 import { getRowStr } from './components/faceted/util';
@@ -36,7 +36,6 @@ export function facetedStateTreeF() {
     })
         .volatile(() => ({
         visible: {},
-        widths: {},
         useShoppingCart: false,
         filters: observable.map(),
     }))
@@ -164,35 +163,10 @@ export function facetedStateTreeF() {
         setVisible(args) {
             self.visible = args;
         },
-        /**
-         * #action
-         */
-        setWidths(args) {
-            self.widths = args;
-        },
         afterAttach() {
             addDisposer(self, autorun(() => {
                 this.setVisible(Object.fromEntries(self.fields.map(c => [c, true])));
             }));
-            addDisposer(self, autorun(() => {
-                this.setWidths({
-                    name: measureGridWidth(self.rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
-                    ...Object.fromEntries(self.filteredNonMetadataKeys
-                        .filter(f => self.visible[f])
-                        .map(e => [
-                        e,
-                        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,
-                            measureGridWidth(self.rows.map(r => r.metadata[e]), { maxWidth: 400, stripHTML: true }),
-                        ];
-                    })),
-                });
-            }));
         },
     }));
 }

package/esm/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/esm/HierarchicalTrackSelectorWidget/index.js

@@ -2,7 +2,7 @@ import stateModelFactory from './model';
 import configSchema from './configSchema';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
 import { lazy } from 'react';
-export default (pluginManager) => {
+export default function HierarchicalTrackSelectorWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new WidgetType({
             name: 'HierarchicalTrackSelectorWidget',
@@ -12,6 +12,6 @@ export default (pluginManager) => {
             ReactComponent: lazy(() => import('./components/HierarchicalTrackSelector')),
         });
     });
-};
+}
 export { default as stateModelFactory, } from './model';
 export { default as configSchema } from './configSchema';

package/esm/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