@jbrowse/plugin-data-management 2.6.3 → 2.7.1

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedHeader.d.ts

@@ -1,13 +1,15 @@
 import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../../model';
-export default function FacetedHeader({ setFilterText, setUseShoppingCart, setHideSparse, setShowOptions, showOptions, hideSparse, useShoppingCart, filterText, model, }: {
+export default function FacetedHeader({ setFilterText, setUseShoppingCart, setShowSparse, setShowFilters, setShowOptions, showOptions, showSparse, showFilters, useShoppingCart, filterText, model, }: {
     setFilterText: (arg: string) => void;
     setUseShoppingCart: (arg: boolean) => void;
-    setHideSparse: (arg: boolean) => void;
+    setShowSparse: (arg: boolean) => void;
+    setShowFilters: (arg: boolean) => void;
     setShowOptions: (arg: boolean) => void;
     filterText: string;
     showOptions: boolean;
     useShoppingCart: boolean;
-    hideSparse: boolean;
+    showSparse: boolean;
+    showFilters: boolean;
     model: HierarchicalTrackSelectorModel;
 }): React.JSX.Element;

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

@@ -6,7 +6,7 @@ import ClearIcon from '@mui/icons-material/Clear';
 import MoreVert from '@mui/icons-material/MoreVert';
 // locals
 import ShoppingCart from '../ShoppingCart';
-export default function FacetedHeader({ setFilterText, setUseShoppingCart, setHideSparse, setShowOptions, showOptions, hideSparse, useShoppingCart, filterText, model, }) {
+export default function FacetedHeader({ setFilterText, setUseShoppingCart, setShowSparse, setShowFilters, setShowOptions, showOptions, showSparse, showFilters, useShoppingCart, filterText, model, }) {
     const [anchorEl, setAnchorEl] = useState(null);
     return (React.createElement(React.Fragment, null,
         React.createElement(Grid, { container: true, spacing: 4, alignItems: "center" },
@@ -32,9 +32,15 @@ export default function FacetedHeader({ setFilterText, setUseShoppingCart, setHi
                     checked: useShoppingCart,
                 },
                 {
-                    label: 'Hide sparse metadata columns',
-                    onClick: () => setHideSparse(!hideSparse),
-                    checked: hideSparse,
+                    label: 'Show sparse metadata columns',
+                    onClick: () => setShowSparse(!showSparse),
+                    checked: showSparse,
+                    type: 'checkbox',
+                },
+                {
+                    label: 'Show facet filters',
+                    onClick: () => setShowFilters(!showFilters),
+                    checked: showFilters,
                     type: 'checkbox',
                 },
                 {

package/esm/HierarchicalTrackSelectorWidget/components/faceted/FacetedSelector.d.ts

@@ -6,7 +6,7 @@ export interface InfoArgs {
     id: string;
     conf: AnyConfigurationModel;
 }
-declare const _default: ({ model, }: {
+declare const FacetedSelector: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
 }) => React.JSX.Element;
-export default _default;
+export default FacetedSelector;

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

@@ -9,9 +9,11 @@ import { getTrackName } from '@jbrowse/core/util/tracks';
 import { ResizeHandle } from '@jbrowse/core/ui';
 import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
 import JBrowseMenu from '@jbrowse/core/ui/Menu';
-import ResizeBar, { useResizeBar } from '@jbrowse/core/ui/ResizeBar';
-import { getEnv, getSession, measureGridWidth, useDebounce, } from '@jbrowse/core/util';
+import ResizeBar from '@jbrowse/core/ui/ResizeBar';
+import { getEnv, getSession, measureGridWidth, useDebounce, useLocalStorage, } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
+import { useResizeBar } from '@jbrowse/core/ui/useResizeBar';
+import { makeStyles } from 'tss-react/mui';
 // icons
 import MoreHoriz from '@mui/icons-material/MoreHoriz';
 import { matches } from '../../util';
@@ -19,24 +21,31 @@ import FacetedHeader from './FacetedHeader';
 import FacetFilters from './FacetFilters';
 import { getRootKeys } from './util';
 const nonMetadataKeys = ['category', 'adapter', 'description'];
+const useStyles = makeStyles()({
+    cell: {
+        whiteSpace: 'nowrap',
+        overflow: 'hidden',
+        textOverflow: 'ellipsis',
+    },
+});
 const frac = 0.75;
-export default observer(function FacetedSelector({ model, }) {
+const FacetedSelector = observer(function FacetedSelector({ model, }) {
     var _a, _b;
+    const { classes } = useStyles();
     const { view, selection } = model;
     const { pluginManager } = getEnv(model);
     const { ref, scrollLeft } = useResizeBar();
     const [filterText, setFilterText] = useState('');
-    const [showOptions, setShowOptions] = useState(false);
+    const [showOptions, setShowOptions] = useLocalStorage('facet-showTableOptions', false);
     const [info, setInfo] = useState();
     const [useShoppingCart, setUseShoppingCart] = useState(false);
-    const [hideSparse, setHideSparse] = useState(true);
-    const [panelWidth, setPanelWidth] = useState(400);
+    const [showSparse, setShowSparse] = useLocalStorage('facet-showSparse', false);
+    const [showFilters, setShowFilters] = useLocalStorage('facet-showFilters', true);
+    const [panelWidth, setPanelWidth] = useLocalStorage('facet-panelWidth', 400);
     const session = getSession(model);
     const filterDebounced = useDebounce(filterText, 400);
     const tracks = view.tracks;
-    const [filters, dispatch] = useReducer((state, update) => {
-        return { ...state, [update.key]: update.val };
-    }, {});
+    const [filters, dispatch] = useReducer((state, update) => ({ ...state, [update.key]: update.val }), {});
     const rows = useMemo(() => {
         // metadata is spread onto the object for easier access and sorting
         // by the mui data grid (it's unable to sort by nested objects)
@@ -57,10 +66,10 @@ export default observer(function FacetedSelector({ model, }) {
             };
         });
     }, [model, filterDebounced, session]);
-    const filteredNonMetadataKeys = useMemo(() => nonMetadataKeys.filter(f => !hideSparse ? true : rows.map(r => r[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
-    const filteredMetadataKeys = useMemo(() => [...new Set(rows.flatMap(row => getRootKeys(row.metadata)))].filter(f => !hideSparse
+    const filteredNonMetadataKeys = useMemo(() => nonMetadataKeys.filter(f => showSparse ? true : rows.map(r => r[f]).filter(f => !!f).length > 5), [showSparse, rows]);
+    const filteredMetadataKeys = useMemo(() => [...new Set(rows.flatMap(row => getRootKeys(row.metadata)))].filter(f => showSparse
         ? true
-        : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
+        : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5), [showSparse, rows]);
     const fields = useMemo(() => ['name', ...filteredNonMetadataKeys, ...filteredMetadataKeys], [filteredNonMetadataKeys, filteredMetadataKeys]);
     const [widths, setWidths] = useState({
         name: measureGridWidth(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
@@ -96,15 +105,15 @@ export default observer(function FacetedSelector({ model, }) {
                 measureGridWidth(rows.map(r => r.metadata[e]), { stripHTML: true, maxWidth: 400 }),
             ])),
         }));
-    }, [filteredMetadataKeys, visible, filteredNonMetadataKeys, hideSparse, rows]);
-    const widthsDebounced = useDebounce(widths, 400);
+    }, [filteredMetadataKeys, visible, filteredNonMetadataKeys, showSparse, rows]);
+    const widthsDebounced = useDebounce(widths, 200);
     const columns = [
         {
             field: 'name',
             hideable: false,
             renderCell: (params) => {
                 const { value, id, row } = params;
-                return (React.createElement(React.Fragment, null,
+                return (React.createElement("div", { className: classes.cell },
                     React.createElement(SanitizedHTML, { html: value }),
                     React.createElement(IconButton, { onClick: e => setInfo({
                             target: e.currentTarget,
@@ -122,7 +131,7 @@ export default observer(function FacetedSelector({ model, }) {
                 width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
                 renderCell: (params) => {
                     const { value } = params;
-                    return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+                    return (React.createElement("div", { className: classes.cell }, value ? React.createElement(SanitizedHTML, { html: value }) : ''));
                 },
             });
         }),
@@ -133,19 +142,22 @@ export default observer(function FacetedSelector({ model, }) {
                 width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
                 renderCell: (params) => {
                     const { value } = params;
-                    return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+                    return (React.createElement("div", { className: classes.cell }, value ? React.createElement(SanitizedHTML, { html: value }) : ''));
                 },
             });
         }),
     ];
-    const shownTrackIds = tracks.map(t => t.configuration.trackId);
-    const arrFilters = Object.entries(filters).filter(f => f[1].length > 0);
+    const shownTrackIds = new Set(tracks.map(t => t.configuration.trackId));
+    const arrFilters = Object.entries(filters)
+        .filter(f => f[1].length > 0)
+        .map(([key, val]) => [key, new Set(val)]);
+    const filteredRows = rows.filter(row => arrFilters.every(([key, val]) => val.has(row[key])));
     return (React.createElement(React.Fragment, null,
         info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: ((_b = session.getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(session, info.conf)) || [], onMenuItemClick: (_event, callback) => {
                 callback();
                 setInfo(undefined);
             }, open: !!info, onClose: () => setInfo(undefined) })) : null,
-        React.createElement(FacetedHeader, { setHideSparse: setHideSparse, setShowOptions: setShowOptions, setFilterText: setFilterText, setUseShoppingCart: setUseShoppingCart, hideSparse: hideSparse, showOptions: showOptions, filterText: filterText, useShoppingCart: useShoppingCart, model: model }),
+        React.createElement(FacetedHeader, { setShowSparse: setShowSparse, setShowFilters: setShowFilters, setShowOptions: setShowOptions, setFilterText: setFilterText, setUseShoppingCart: setUseShoppingCart, showFilters: showFilters, showSparse: showSparse, showOptions: showOptions, filterText: filterText, useShoppingCart: useShoppingCart, model: model }),
         React.createElement("div", { ref: ref, style: {
                 display: 'flex',
                 overflow: 'hidden',
@@ -154,21 +166,22 @@ export default observer(function FacetedSelector({ model, }) {
             } },
             React.createElement("div", { style: {
                     height: window.innerHeight * frac,
-                    width: window.innerWidth * frac - panelWidth,
+                    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 => setWidths(Object.fromEntries(Object.entries(widths).map((entry, idx) => [
                         entry[0],
                         newWidths[idx],
                     ]))), scrollLeft: scrollLeft }),
-                React.createElement(DataGrid, { rows: rows.filter(row => arrFilters.every(([key, val]) => val.includes(row[key]))), columnVisibilityModel: visible, onColumnVisibilityModelChange: newModel => setVisible(newModel), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
+                React.createElement(DataGrid, { rows: filteredRows, columnVisibilityModel: visible, onColumnVisibilityModelChange: newModel => setVisible(newModel), columnHeaderHeight: 35, checkboxSelection: true, disableRowSelectionOnClick: true, keepNonExistentRowsSelected: true, onRowSelectionModelChange: userSelectedIds => {
                         if (!useShoppingCart) {
                             const a1 = shownTrackIds;
-                            const a2 = userSelectedIds;
+                            const a2 = new Set(userSelectedIds);
                             // synchronize the user selection with the view
                             // see share https://stackoverflow.com/a/33034768/2129219
                             transaction(() => {
-                                a1.filter(x => !a2.includes(x)).map(t => view.hideTrack(t));
-                                a2.filter(x => !a1.includes(x)).map(t => view.showTrack(t));
+                                ;
+                                [...a1].filter(x => !a2.has(x)).map(t => view.hideTrack(t));
+                                [...a2].filter(x => !a1.has(x)).map(t => view.showTrack(t));
                             });
                         }
                         else {
@@ -177,10 +190,18 @@ export default observer(function FacetedSelector({ model, }) {
                             const tracks = userSelectedIds.map(id => resolveIdentifier(schema, root, id));
                             model.setSelection(tracks);
                         }
-                    }, rowSelectionModel: useShoppingCart ? selection.map(s => s.trackId) : shownTrackIds, slots: { toolbar: showOptions ? GridToolbar : null }, slotProps: {
+                    }, rowSelectionModel: useShoppingCart
+                        ? selection.map(s => s.trackId)
+                        : [...shownTrackIds], slots: { toolbar: showOptions ? GridToolbar : null }, slotProps: {
                         toolbar: { printOptions: { disableToolbarButton: true } },
                     }, columns: columns, rowHeight: 25 })),
-            React.createElement(ResizeHandle, { vertical: true, onDrag: dist => setPanelWidth(panelWidth - dist), style: { background: 'grey', width: 5 } }),
-            React.createElement("div", { style: { width: panelWidth, overflowY: 'auto', overflowX: 'hidden' } },
-                React.createElement(FacetFilters, { width: panelWidth - 10, rows: rows, columns: columns, dispatch: dispatch, filters: filters })))));
+            showFilters ? (React.createElement(React.Fragment, null,
+                React.createElement(ResizeHandle, { vertical: true, onDrag: dist => setPanelWidth(panelWidth - dist), style: { marginLeft: 5, background: 'grey', width: 5 } }),
+                React.createElement("div", { style: {
+                        width: panelWidth,
+                        overflowY: 'auto',
+                        overflowX: 'hidden',
+                    } },
+                    React.createElement(FacetFilters, { width: panelWidth - 10, rows: rows, columns: columns, dispatch: dispatch, filters: filters })))) : null)));
 });
+export default FacetedSelector;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../../model';
-declare const _default: ({ model, }: {
+declare const HamburgerMenu: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
 }) => React.JSX.Element;
-export default _default;
+export default HamburgerMenu;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.js

@@ -10,15 +10,16 @@ const CloseConnectionDlg = lazy(() => import('../dialogs/CloseConnectionDialog')
 const DeleteConnectionDlg = lazy(() => import('../dialogs/DeleteConnectionDialog'));
 const ManageConnectionsDlg = lazy(() => import('../dialogs/ManageConnectionsDialog'));
 const ToggleConnectionsDlg = lazy(() => import('../dialogs/ToggleConnectionsDialog'));
-export default observer(function HamburgerMenu({ model, }) {
+const HamburgerMenu = observer(function ({ model, }) {
     const session = getSession(model);
     const [modalInfo, setModalInfo] = useState();
     const [deleteDlgDetails, setDeleteDlgDetails] = useState();
     const [connectionToggleOpen, setConnectionToggleOpen] = useState(false);
     const [connectionManagerOpen, setConnectionManagerOpen] = useState(false);
     function breakConnection(connectionConf, deletingConnection) {
+        var _a;
         const name = readConfObject(connectionConf, 'name');
-        const result = session.prepareToBreakConnection(connectionConf);
+        const result = (_a = session.prepareToBreakConnection) === null || _a === void 0 ? void 0 : _a.call(session, connectionConf);
         if (result) {
             const [safelyBreakConnection, dereferenceTypeCount] = result;
             if (Object.keys(dereferenceTypeCount).length > 0) {
@@ -115,3 +116,4 @@ export default observer(function HamburgerMenu({ model, }) {
             connectionManagerOpen ? (React.createElement(ManageConnectionsDlg, { handleClose: () => setConnectionManagerOpen(false), breakConnection: breakConnection, session: session })) : null,
             connectionToggleOpen ? (React.createElement(ToggleConnectionsDlg, { handleClose: () => setConnectionToggleOpen(false), session: session, breakConnection: breakConnection })) : null)));
 });
+export default HamburgerMenu;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.d.ts

@@ -1,8 +1,7 @@
 import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../../model';
-declare function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }: {
+declare const HierarchicalTrackSelectorHeader: ({ model, setHeaderHeight, }: {
     model: HierarchicalTrackSelectorModel;
     setHeaderHeight: (n: number) => void;
-}): React.JSX.Element;
-declare const _default: typeof HierarchicalTrackSelectorHeader;
-export default _default;
+}) => React.JSX.Element;
+export default HierarchicalTrackSelectorHeader;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalHeader.js

@@ -26,7 +26,7 @@ const SearchTracksTextField = observer(function ({ model, }) {
                     React.createElement(ClearIcon, null)))),
         } }));
 });
-function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }) {
+const HierarchicalTrackSelectorHeader = observer(function ({ model, setHeaderHeight, }) {
     const { classes } = useStyles();
     const [facetedOpen, setFacetedOpen] = useState(false);
     return (React.createElement("div", { ref: ref => setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0), "data-testid": "hierarchical_track_selector" },
@@ -36,5 +36,5 @@ function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }) {
             React.createElement(SearchTracksTextField, { model: model }),
             React.createElement(Button, { className: classes.menuIcon, onClick: () => setFacetedOpen(true) }, "Open faceted selector")),
         React.createElement(Suspense, { fallback: React.createElement("div", null) }, facetedOpen ? (React.createElement(FacetedDialog, { handleClose: () => setFacetedOpen(false), model: model })) : null)));
-}
-export default observer(HierarchicalTrackSelectorHeader);
+});
+export default HierarchicalTrackSelectorHeader;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.d.ts

@@ -1,9 +1,9 @@
 import React from 'react';
 import { TreeNode } from '../../generateHierarchy';
 import { HierarchicalTrackSelectorModel } from '../../model';
-declare const _default: ({ height, tree, model, }: {
+declare const HierarchicalTree: ({ height, tree, model, }: {
     height: number;
     tree: TreeNode;
     model: HierarchicalTrackSelectorModel;
 }) => React.JSX.Element;
-export default _default;
+export default HierarchicalTree;

package/esm/HierarchicalTrackSelectorWidget/components/tree/HierarchicalTree.js

@@ -23,7 +23,7 @@ function getNodeData(node, nestingLevel, extra, selection) {
 // this is the main tree component for the hierarchical track selector in note:
 // in jbrowse-web the toolbar is position="sticky" which means the autosizer
 // includes the height of the toolbar, so we subtract the given offsets
-export default observer(function HierarchicalTree({ height, tree, model, }) {
+const HierarchicalTree = observer(function HierarchicalTree({ height, tree, model, }) {
     const { filterText, selection, view } = model;
     const treeRef = useRef(null);
     const session = getSession(model);
@@ -37,15 +37,13 @@ export default observer(function HierarchicalTree({ height, tree, model, }) {
         drawerPosition,
     }), [view, model, drawerPosition, tree]);
     const treeWalker = useCallback(function* treeWalker() {
-        for (let i = 0; i < tree.children.length; i++) {
-            const r = tree.children[i];
-            yield getNodeData(r, 0, extra, obj);
+        for (const child of tree.children) {
+            yield getNodeData(child, 0, extra, obj);
         }
         while (true) {
             // @ts-expect-error
             const parentMeta = yield;
-            for (let i = 0; i < parentMeta.node.children.length; i++) {
-                const curr = parentMeta.node.children[i];
+            for (const curr of parentMeta.node.children) {
                 yield getNodeData(curr, parentMeta.nestingLevel + 1, extra, obj);
             }
         }
@@ -60,3 +58,4 @@ export default observer(function HierarchicalTree({ height, tree, model, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, Node)));
 });
+export default HierarchicalTree;

package/esm/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js

@@ -1,14 +1,14 @@
-import React, { useState } from 'react';
-import { Checkbox, FormControlLabel, IconButton, Tooltip } from '@mui/material';
+import React from 'react';
+import { Checkbox, FormControlLabel, Tooltip } from '@mui/material';
 import { makeStyles } from 'tss-react/mui';
-import JBrowseMenu from '@jbrowse/core/ui/Menu';
 import { getSession } from '@jbrowse/core/util';
+import SanitizedHTML from '@jbrowse/core/ui/SanitizedHTML';
 import { readConfObject, } from '@jbrowse/core/configuration';
 // icons
 import MoreHorizIcon from '@mui/icons-material/MoreHoriz';
 // locals
 import { isUnsupported } from '../util';
-import { SanitizedHTML } from '@jbrowse/core/ui';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 const useStyles = makeStyles()(theme => ({
     compactCheckbox: {
         padding: 0,
@@ -21,10 +21,8 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 export default function TrackLabel({ data }) {
-    var _a, _b;
     const { classes } = useStyles();
     const { checked, conf, model, drawerPosition, id, name, onChange, selected } = data;
-    const [info, setInfo] = useState();
     const description = (conf && readConfObject(conf, ['description'])) || '';
     return (React.createElement(React.Fragment, null,
         React.createElement(Tooltip, { title: description + (selected ? ' (in selection)' : ''), placement: drawerPosition === 'left' ? 'right' : 'left' },
@@ -33,24 +31,24 @@ export default function TrackLabel({ data }) {
                         'data-testid': `htsTrackEntry-${id}`,
                     } }), label: React.createElement("div", { "data-testid": `htsTrackLabel-${id}`, style: { background: selected ? '#cccc' : undefined } },
                     React.createElement(SanitizedHTML, { html: name })) })),
-        React.createElement(IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
-            React.createElement(MoreHorizIcon, null)),
-        info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [
-                ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, info.conf)) || []),
-                {
-                    label: 'Add to selection',
-                    onClick: () => model.addToSelection([info.conf]),
-                },
-                ...(selected
-                    ? [
-                        {
-                            label: 'Remove from selection',
-                            onClick: () => model.removeFromSelection([info.conf]),
-                        },
-                    ]
-                    : []),
-            ], onMenuItemClick: (_event, callback) => {
-                callback();
-                setInfo(undefined);
-            }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
+        React.createElement(TrackMenuButton, { model: model, selected: selected, id: id, conf: conf })));
+}
+function TrackMenuButton({ id, model, selected, conf, }) {
+    var _a, _b;
+    return (React.createElement(CascadingMenuButton, { style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}`, menuItems: [
+            ...(((_b = (_a = getSession(model)).getTrackActionMenuItems) === null || _b === void 0 ? void 0 : _b.call(_a, conf)) || []),
+            {
+                label: 'Add to selection',
+                onClick: () => model.addToSelection([conf]),
+            },
+            ...(selected
+                ? [
+                    {
+                        label: 'Remove from selection',
+                        onClick: () => model.removeFromSelection([conf]),
+                    },
+                ]
+                : []),
+        ] },
+        React.createElement(MoreHorizIcon, null)));
 }

package/esm/HierarchicalTrackSelectorWidget/components/util.js

@@ -6,8 +6,7 @@ export function treeToMap(tree, map = new Map()) {
     if (tree.id && tree.children.length) {
         map.set(tree.id, tree);
     }
-    for (let i = 0; i < tree.children.length; i++) {
-        const node = tree.children[i];
+    for (const node of tree.children) {
         treeToMap(node, map);
     }
     return map;

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts

@@ -1,21 +1,24 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-export type TreeNode = {
+export interface TreeNode {
     name: string;
     id: string;
     conf?: AnyConfigurationModel;
     checked?: boolean;
     isOpenByDefault?: boolean;
     children: TreeNode[];
-};
-export declare function generateHierarchy(model: {
-    filterText: string;
-    activeSortTrackNames: boolean;
-    activeSortCategories: boolean;
-    view?: {
-        tracks: {
-            configuration: AnyConfigurationModel;
-        }[];
+}
+export declare function generateHierarchy({ model, trackConfs, extra, }: {
+    model: {
+        filterText: string;
+        activeSortTrackNames: boolean;
+        activeSortCategories: boolean;
+        collapsed: Map<string, boolean>;
+        view?: {
+            tracks: {
+                configuration: AnyConfigurationModel;
+            }[];
+        };
     };
-}, trackConfs: AnyConfigurationModel[], collapsed: {
-    get: (arg: string) => boolean | undefined;
-}, extra?: string): TreeNode[];
+    trackConfs: AnyConfigurationModel[];
+    extra?: string;
+}): TreeNode[];

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -37,9 +37,9 @@ function sortConfs(confs, sortNames, sortCategories) {
     }
     return ret.map(a => a[0]);
 }
-export function generateHierarchy(model, trackConfs, collapsed, extra) {
+export function generateHierarchy({ model, trackConfs, extra, }) {
     const hierarchy = { children: [] };
-    const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
+    const { collapsed, filterText, activeSortTrackNames, activeSortCategories, view, } = model;
     if (!view) {
         return [];
     }

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -186,7 +186,11 @@ export default function stateTreeFactory(pluginManager) {
          * #method
          */
         connectionHierarchy(connection) {
-            return generateHierarchy(self, self.connectionTrackConfigurations(connection), self.collapsed, connection.name);
+            return generateHierarchy({
+                model: self,
+                trackConfs: self.connectionTrackConfigurations(connection),
+                extra: connection.name,
+            });
         },
     }))
         .views(self => ({
@@ -216,7 +220,10 @@ export default function stateTreeFactory(pluginManager) {
                     .map(s => ({
                     name: s.group,
                     id: s.group,
-                    children: generateHierarchy(self, s.tracks, self.collapsed),
+                    children: generateHierarchy({
+                        model: self,
+                        trackConfs: s.tracks,
+                    }),
                 }))
                     // always keep the Tracks entry at idx 0
                     .filter((f, idx) => idx === 0 || !!f.children.length),
@@ -260,21 +267,19 @@ export default function stateTreeFactory(pluginManager) {
                 ])) {
                     self.collapseTopLevelCategories();
                 }
-                else if (getConf(session, [
+                if (getConf(session, [
                     'hierarchical',
                     'defaultCollapsed',
                     'subCategories',
                 ])) {
                     self.collapseSubCategories();
                 }
-                else {
-                    for (const entry of getConf(session, [
-                        'hierarchical',
-                        'defaultCollapsed',
-                        'categoryNames',
-                    ])) {
-                        self.collapsed.set(entry, true);
-                    }
+                for (const entry of getConf(session, [
+                    'hierarchical',
+                    'defaultCollapsed',
+                    'categoryNames',
+                ])) {
+                    self.collapsed.set(entry, true);
                 }
                 self.initialized = true;
             }
@@ -282,7 +287,7 @@ export default function stateTreeFactory(pluginManager) {
     }))
         .views(self => ({
         get hasAnySubcategories() {
-            return self.allTracks.some(group => group.tracks.some(track => { var _a; return ((_a = readConfObject(track, 'category')) === null || _a === void 0 ? void 0 : _a.length) > 1; }));
+            return self.allTracks.some(group => group.tracks.some(t => { var _a; return ((_a = readConfObject(t, 'category')) === null || _a === void 0 ? void 0 : _a.length) > 1; }));
         },
     }));
 }

package/esm/PluginStoreWidget/components/AddCustomPluginDialog.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
 import { PluginStoreModel } from '../model';
-declare const _default: ({ onClose, model, }: {
+declare const AddCustomPluginDialog: ({ onClose, model, }: {
     onClose: () => void;
     model: PluginStoreModel;
 }) => React.JSX.Element;
-export default _default;
+export default AddCustomPluginDialog;

package/esm/PluginStoreWidget/components/AddCustomPluginDialog.js

@@ -23,7 +23,7 @@ const useStyles = makeStyles()(theme => ({
         transform: 'rotate(180deg)',
     },
 }));
-export default observer(function ({ onClose, model, }) {
+const AddCustomPluginDialog = observer(function ({ onClose, model, }) {
     const { classes, cx } = useStyles();
     const [umdPluginName, setUMDPluginName] = useState('');
     const [umdPluginUrl, setUMDPluginUrl] = useState('');
@@ -64,3 +64,4 @@ export default observer(function ({ onClose, model, }) {
                 React.createElement(Button, { variant: "contained", onClick: onClose }, "Cancel"),
                 React.createElement(Button, { variant: "contained", color: "primary", onClick: handleSubmit, disabled: !ready }, "Submit")))));
 });
+export default AddCustomPluginDialog;

package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
 import { BasePlugin } from '@jbrowse/core/util/types';
 import { PluginStoreModel } from '../model';
-declare const _default: ({ plugin, model, }: {
+declare const InstalledPlugin: ({ plugin, model, }: {
     plugin: BasePlugin;
     model: PluginStoreModel;
 }) => React.JSX.Element;
-export default _default;
+export default InstalledPlugin;

package/esm/PluginStoreWidget/components/InstalledPlugin.js

@@ -18,12 +18,15 @@ function LockedPlugin() {
     return (React.createElement(Tooltip, { className: classes.lockedPluginTooltip, title: "This plugin was installed by an administrator, you cannot remove it." },
         React.createElement(LockIcon, null)));
 }
-export default observer(function ({ plugin, model, }) {
+const InstalledPlugin = observer(function ({ plugin, model, }) {
+    var _a;
     const [dialogPlugin, setDialogPlugin] = useState();
     const { pluginManager } = getEnv(model);
     const session = getSession(model);
-    const { jbrowse, adminMode, sessionPlugins } = session;
-    const isSessionPlugin = sessionPlugins === null || sessionPlugins === void 0 ? void 0 : sessionPlugins.some((p) => pluginManager.pluginMetadata[plugin.name].url === p.url);
+    const { jbrowse, adminMode } = session;
+    const isSessionPlugin = isSessionWithSessionPlugins(session)
+        ? (_a = session.sessionPlugins) === null || _a === void 0 ? void 0 : _a.some(p => pluginManager.pluginMetadata[plugin.name].url === p.url)
+        : false;
     return (React.createElement(React.Fragment, null,
         dialogPlugin ? (React.createElement(Suspense, { fallback: React.createElement(React.Fragment, null) },
             React.createElement(DeletePluginDialog, { plugin: dialogPlugin, onClose: name => {
@@ -39,7 +42,8 @@ export default observer(function ({ plugin, model, }) {
                     setDialogPlugin(undefined);
                 } }))) : null,
         React.createElement(ListItem, { key: plugin.name },
-            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "aria-label": "removePlugin", "data-testid": `removePlugin-${plugin.name}`, onClick: () => setDialogPlugin(plugin.name) },
+            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => setDialogPlugin(plugin.name) },
                 React.createElement(CloseIcon, null))) : (React.createElement(LockedPlugin, null)),
             React.createElement(Typography, null, plugin.name))));
 });
+export default InstalledPlugin;

package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts

@@ -1,8 +1,8 @@
 import React from 'react';
 import PluginManager from '@jbrowse/core/PluginManager';
 import { PluginStoreModel } from '../model';
-declare const _default: ({ pluginManager, model, }: {
+declare const InstalledPluginsList: ({ pluginManager, model, }: {
     pluginManager: PluginManager;
     model: PluginStoreModel;
 }) => React.JSX.Element;
-export default _default;
+export default InstalledPluginsList;