@jbrowse/plugin-data-management 2.6.2 → 2.7.0

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

@@ -9,35 +9,43 @@ 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';
-// locals
-import { matches } from '../../model';
+import { matches } from '../../util';
 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)
@@ -58,10 +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,
@@ -97,15 +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,
@@ -123,7 +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 }) : ''));
                 },
             });
         }),
@@ -134,19 +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',
@@ -155,21 +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 {
@@ -178,10 +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

@@ -1,10 +1,8 @@
 import React, { Suspense, lazy, useState } from 'react';
-import { IconButton } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
-import JBrowseMenu from '@jbrowse/core/ui/Menu';
 import { getSession, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
+import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton';
 // icons
 import MenuIcon from '@mui/icons-material/Menu';
 // lazy components
@@ -12,23 +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'));
-const useStyles = makeStyles()(theme => ({
-    menuIcon: {
-        marginRight: theme.spacing(1),
-        marginBottom: 0,
-    },
-}));
-export default observer(function HamburgerMenu({ model, }) {
+const HamburgerMenu = observer(function ({ model, }) {
     const session = getSession(model);
-    const [menuEl, setMenuEl] = useState();
     const [modalInfo, setModalInfo] = useState();
     const [deleteDlgDetails, setDeleteDlgDetails] = useState();
     const [connectionToggleOpen, setConnectionToggleOpen] = useState(false);
     const [connectionManagerOpen, setConnectionManagerOpen] = useState(false);
-    const { classes } = useStyles();
     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) {
@@ -48,12 +39,7 @@ export default observer(function HamburgerMenu({ model, }) {
         }
     }
     return (React.createElement(React.Fragment, null,
-        React.createElement(IconButton, { className: classes.menuIcon, onClick: event => setMenuEl(event.currentTarget) },
-            React.createElement(MenuIcon, null)),
-        React.createElement(JBrowseMenu, { anchorEl: menuEl, open: Boolean(menuEl), onMenuItemClick: (_, callback) => {
-                callback();
-                setMenuEl(undefined);
-            }, onClose: () => setMenuEl(undefined), menuItems: [
+        React.createElement(CascadingMenuButton, { menuItems: [
                 ...(isSessionWithAddTracks(session)
                     ? [
                         {
@@ -92,10 +78,42 @@ export default observer(function HamburgerMenu({ model, }) {
                         },
                     ]
                     : []),
-            ] }),
+                { type: 'divider' },
+                {
+                    label: 'Sort tracks by name',
+                    type: 'checkbox',
+                    checked: model.activeSortTrackNames,
+                    onClick: () => model.setSortTrackNames(!model.activeSortTrackNames),
+                },
+                {
+                    label: 'Sort categories by name',
+                    type: 'checkbox',
+                    checked: model.activeSortCategories,
+                    onClick: () => model.setSortCategories(!model.activeSortCategories),
+                },
+                { type: 'divider' },
+                ...(model.hasAnySubcategories
+                    ? [
+                        {
+                            label: 'Collapse subcategories',
+                            onClick: () => model.collapseSubCategories(),
+                        },
+                    ]
+                    : []),
+                {
+                    label: 'Collapse top-level categories',
+                    onClick: () => model.collapseTopLevelCategories(),
+                },
+                {
+                    label: 'Expand all categories',
+                    onClick: () => model.expandAllCategories(),
+                },
+            ] },
+            React.createElement(MenuIcon, null)),
         React.createElement(Suspense, { fallback: React.createElement(React.Fragment, null) },
             modalInfo ? (React.createElement(CloseConnectionDlg, { modalInfo: modalInfo, onClose: () => setModalInfo(undefined) })) : null,
             deleteDlgDetails ? (React.createElement(DeleteConnectionDlg, { handleClose: () => setDeleteDlgDetails(undefined), deleteDialogDetails: deleteDlgDetails, session: session })) : null,
             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

@@ -17,20 +17,24 @@ const useStyles = makeStyles()(theme => ({
         marginBottom: 0,
     },
 }));
-function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, }) {
+const SearchTracksTextField = observer(function ({ model, }) {
+    const { filterText } = model;
+    const { classes } = useStyles();
+    return (React.createElement(TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
+            endAdornment: (React.createElement(InputAdornment, { position: "end" },
+                React.createElement(IconButton, { onClick: () => model.clearFilterText() },
+                    React.createElement(ClearIcon, null)))),
+        } }));
+});
+const HierarchicalTrackSelectorHeader = observer(function ({ model, setHeaderHeight, }) {
     const { classes } = useStyles();
     const [facetedOpen, setFacetedOpen] = useState(false);
-    const { filterText } = model;
     return (React.createElement("div", { ref: ref => setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0), "data-testid": "hierarchical_track_selector" },
         React.createElement("div", { style: { display: 'flex' } },
             React.createElement(HamburgerMenu, { model: model }),
             React.createElement(ShoppingCart, { model: model }),
-            React.createElement(TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => model.setFilterText(event.target.value), fullWidth: true, InputProps: {
-                    endAdornment: (React.createElement(InputAdornment, { position: "end" },
-                        React.createElement(IconButton, { onClick: () => model.clearFilterText() },
-                            React.createElement(ClearIcon, null)))),
-                } }),
+            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

@@ -1,8 +1,9 @@
 import React from 'react';
-import { TreeNode, HierarchicalTrackSelectorModel } from '../../model';
-declare const _default: ({ height, tree, model, }: {
+import { TreeNode } from '../../generateHierarchy';
+import { HierarchicalTrackSelectorModel } from '../../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/TrackCategory.js

@@ -52,6 +52,28 @@ export default function Category({ isOpen, setOpen, data, }) {
                         model.removeFromSelection(getAllChildren(r));
                     },
                 },
+                {
+                    label: 'Show all tracks',
+                    onClick: () => {
+                        var _a;
+                        for (const entry of ((_a = treeToMap(tree).get(id)) === null || _a === void 0 ? void 0 : _a.children) || []) {
+                            if (!entry.children.length) {
+                                model.view.showTrack(entry.id);
+                            }
+                        }
+                    },
+                },
+                {
+                    label: 'Hide all tracks',
+                    onClick: () => {
+                        var _a;
+                        for (const entry of ((_a = treeToMap(tree).get(id)) === null || _a === void 0 ? void 0 : _a.children) || []) {
+                            if (!entry.children.length) {
+                                model.view.hideTrack(entry.id);
+                            }
+                        }
+                    },
+                },
             ], onMenuItemClick: (_event, callback) => {
                 callback();
                 setMenuEl(null);

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

@@ -3,12 +3,12 @@ import { Checkbox, FormControlLabel, IconButton, 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';
 const useStyles = makeStyles()(theme => ({
     compactCheckbox: {
         padding: 0,
@@ -31,7 +31,7 @@ export default function TrackLabel({ data }) {
             React.createElement(FormControlLabel, { className: classes.checkboxLabel, control: React.createElement(Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: isUnsupported(name), inputProps: {
                         // @ts-expect-error
                         'data-testid': `htsTrackEntry-${id}`,
-                    } }), label: React.createElement("div", { style: { background: selected ? '#cccc' : undefined } },
+                    } }), label: React.createElement("div", { "data-testid": `htsTrackLabel-${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)),

package/esm/HierarchicalTrackSelectorWidget/components/util.d.ts

@@ -1,5 +1,6 @@
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { HierarchicalTrackSelectorModel, TreeNode } from '../model';
+import { HierarchicalTrackSelectorModel } from '../model';
+import { TreeNode } from '../generateHierarchy';
 export interface NodeData {
     nestingLevel: number;
     checked: boolean;

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/filterTracks.d.ts

@@ -0,0 +1,12 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function filterTracks(tracks: AnyConfigurationModel[], self: {
+    view?: {
+        type: string;
+        trackSelectorAnyOverlap?: boolean;
+    };
+    assemblyNames: string[];
+}): ({
+    [x: string]: any;
+} & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    setSubschema(slotName: string, data: unknown): any;
+} & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];

package/esm/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -0,0 +1,28 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { getEnv, getSession, notEmpty } from '@jbrowse/core/util';
+import { hasAllOverlap, hasAnyOverlap } from './util';
+export function filterTracks(tracks, self) {
+    const { assemblyManager } = getSession(self);
+    const { pluginManager } = getEnv(self);
+    const { view } = self;
+    if (!view) {
+        return [];
+    }
+    const trackListAssemblies = self.assemblyNames
+        .map(a => assemblyManager.get(a))
+        .filter(notEmpty);
+    return tracks
+        .filter(c => {
+        const trackAssemblyNames = readConfObject(c, 'assemblyNames');
+        const trackAssemblies = trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(notEmpty);
+        return view.trackSelectorAnyOverlap
+            ? hasAnyOverlap(trackAssemblies, trackListAssemblies)
+            : hasAllOverlap(trackAssemblies, trackListAssemblies);
+    })
+        .filter(c => {
+        const { displayTypes } = pluginManager.getViewType(view.type);
+        const compatDisplays = displayTypes.map(d => d.name);
+        const trackDisplays = c.displays.map((d) => d.type);
+        return hasAnyOverlap(compatDisplays, trackDisplays);
+    });
+}

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts

@@ -0,0 +1,21 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+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;
+        }[];
+    };
+}, trackConfs: AnyConfigurationModel[], collapsed: {
+    get: (arg: string) => boolean | undefined;
+}, extra?: string): TreeNode[];

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -0,0 +1,94 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { getTrackName } from '@jbrowse/core/util/tracks';
+// locals
+import { matches } from './util';
+function sortConfs(confs, sortNames, sortCategories) {
+    // uses readConfObject instead of getTrackName so that the undefined
+    // reference sequence track is sorted to the top
+    const ret = confs.map(c => {
+        var _a, _b, _c;
+        return [
+            c,
+            readConfObject(c, 'name'),
+            ((_a = readConfObject(c, 'category')) === null || _a === void 0 ? void 0 : _a[0]) || '',
+            ((_b = readConfObject(c, 'category')) === null || _b === void 0 ? void 0 : _b[1]) || '',
+            ((_c = readConfObject(c, 'category')) === null || _c === void 0 ? void 0 : _c[2]) || '',
+        ];
+    });
+    if (sortNames) {
+        ret.sort((a, b) => a[1].localeCompare(b[1]));
+    }
+    if (sortCategories) {
+        // sort up to three sub-category levels, harder to code it to go deeper
+        // than this and likely rarely used
+        ret.sort((a, b) => {
+            if (a[2] !== b[2]) {
+                return a[2].localeCompare(b[2]);
+            }
+            else if (a[3] !== b[3]) {
+                return a[3].localeCompare(b[3]);
+            }
+            else if (a[4] !== b[4]) {
+                return a[4].localeCompare(b[4]);
+            }
+            return 0;
+        });
+    }
+    return ret.map(a => a[0]);
+}
+export function generateHierarchy(model, trackConfs, collapsed, extra) {
+    const hierarchy = { children: [] };
+    const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
+    if (!view) {
+        return [];
+    }
+    const session = getSession(model);
+    const viewTracks = view.tracks;
+    const confs = trackConfs.filter(conf => matches(filterText, conf, session));
+    // uses getConf
+    for (const conf of sortConfs(confs, activeSortTrackNames, activeSortCategories)) {
+        // copy the categories since this array can be mutated downstream
+        const categories = [...(readConfObject(conf, 'category') || [])];
+        // hack where if trackId ends with sessionTrack, then push it to a
+        // category that starts with a space to force sort to the top
+        if (conf.trackId.endsWith('sessionTrack')) {
+            categories.unshift(' Session tracks');
+        }
+        let currLevel = hierarchy;
+        // find existing category to put track into or create it
+        for (let i = 0; i < categories.length; i++) {
+            const category = categories[i];
+            const ret = currLevel.children.find(c => c.name === category);
+            const id = [extra, categories.slice(0, i + 1).join(',')]
+                .filter(f => !!f)
+                .join('-');
+            if (!ret) {
+                const n = {
+                    children: [],
+                    name: category,
+                    id,
+                    isOpenByDefault: !collapsed.get(id),
+                };
+                currLevel.children.push(n);
+                currLevel = n;
+            }
+            else {
+                currLevel = ret;
+            }
+        }
+        // uses splice to try to put all leaf nodes above "category nodes" if you
+        // change the splice to a simple push and open
+        // test_data/test_order/config.json you will see the weirdness
+        const r = currLevel.children.findIndex(elt => elt.children.length);
+        const idx = r === -1 ? currLevel.children.length : r;
+        currLevel.children.splice(idx, 0, {
+            id: conf.trackId,
+            name: getTrackName(conf, session),
+            conf,
+            checked: viewTracks.some(f => f.configuration === conf),
+            children: [],
+        });
+    }
+    return hierarchy.children;
+}