@jbrowse/plugin-data-management 2.17.0 → 3.0.0

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

@@ -15,27 +15,35 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __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 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const CascadingMenuButton_1 = __importDefault(require("@jbrowse/core/ui/CascadingMenuButton"));
-// icons
+const util_1 = require("@jbrowse/core/util");
 const Menu_1 = __importDefault(require("@mui/icons-material/Menu"));
-// lazies
+const mobx_react_1 = require("mobx-react");
 const FacetedDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../faceted/FacetedDialog'))));
-// lazy components
 const CloseConnectionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/CloseConnectionDialog'))));
 const DeleteConnectionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/DeleteConnectionDialog'))));
 const ManageConnectionsDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../dialogs/ManageConnectionsDialog'))));
@@ -69,128 +77,120 @@ const HamburgerMenu = (0, mobx_react_1.observer)(function ({ model, }) {
             setDeleteDialogDetails({ name, connectionConf });
         }
     }
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(CascadingMenuButton_1.default, { menuItems: [
-                {
-                    label: 'Open faceted track selector',
-                    onClick: () => {
-                        setFacetedOpen(true);
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(CascadingMenuButton_1.default, { menuItems: [
+                    {
+                        label: 'Open faceted track selector',
+                        onClick: () => {
+                            setFacetedOpen(true);
+                        },
                     },
-                },
-                ...((0, util_1.isSessionWithAddTracks)(session)
-                    ? [
-                        {
-                            label: 'Add track...',
-                            onClick: () => {
-                                if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                                    session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
-                                        view: model.view.id,
-                                    }));
-                                }
+                    ...((0, util_1.isSessionWithAddTracks)(session)
+                        ? [
+                            {
+                                label: 'Add track...',
+                                onClick: () => {
+                                    if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                                        session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                            view: model.view.id,
+                                        }));
+                                    }
+                                },
                             },
-                        },
-                    ]
-                    : []),
-                {
-                    label: 'Connections...',
-                    subMenu: [
-                        ...((0, util_1.isSessionModelWithConnections)(session)
-                            ? [
-                                {
-                                    label: 'Turn on/off connections...',
-                                    onClick: () => {
-                                        setConnectionToggleOpen(true);
+                        ]
+                        : []),
+                    {
+                        label: 'Connections...',
+                        subMenu: [
+                            ...((0, util_1.isSessionModelWithConnections)(session)
+                                ? [
+                                    {
+                                        label: 'Turn on/off connections...',
+                                        onClick: () => {
+                                            setConnectionToggleOpen(true);
+                                        },
                                     },
-                                },
-                            ]
-                            : []),
-                        ...((0, util_1.isSessionModelWithConnectionEditing)(session)
-                            ? [
-                                {
-                                    label: 'Add connection...',
-                                    onClick: () => {
-                                        if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                                            session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
-                                        }
+                                ]
+                                : []),
+                            ...((0, util_1.isSessionModelWithConnectionEditing)(session)
+                                ? [
+                                    {
+                                        label: 'Add connection...',
+                                        onClick: () => {
+                                            if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                                                session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                                            }
+                                        },
                                     },
-                                },
-                                {
-                                    label: 'Delete connections...',
-                                    onClick: () => {
-                                        setConnectionManagerOpen(true);
+                                    {
+                                        label: 'Delete connections...',
+                                        onClick: () => {
+                                            setConnectionManagerOpen(true);
+                                        },
                                     },
+                                ]
+                                : []),
+                        ],
+                    },
+                    {
+                        label: 'Sort...',
+                        type: 'subMenu',
+                        subMenu: [
+                            {
+                                label: 'Sort tracks by name',
+                                type: 'checkbox',
+                                checked: model.activeSortTrackNames,
+                                onClick: () => {
+                                    model.setSortTrackNames(!model.activeSortTrackNames);
                                 },
-                            ]
-                            : []),
-                    ],
-                },
-                {
-                    label: 'Sort...',
-                    type: 'subMenu',
-                    subMenu: [
-                        {
-                            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);
+                            {
+                                label: 'Sort categories by name',
+                                type: 'checkbox',
+                                checked: model.activeSortCategories,
+                                onClick: () => {
+                                    model.setSortCategories(!model.activeSortCategories);
+                                },
                             },
-                        },
-                    ],
-                },
-                {
-                    label: 'Collapse...',
-                    type: 'subMenu',
-                    subMenu: [
-                        ...(model.hasAnySubcategories
-                            ? [
-                                {
-                                    label: 'Collapse subcategories',
-                                    onClick: () => {
-                                        model.collapseSubCategories();
+                        ],
+                    },
+                    {
+                        label: 'Collapse...',
+                        type: 'subMenu',
+                        subMenu: [
+                            ...(model.hasAnySubcategories
+                                ? [
+                                    {
+                                        label: 'Collapse subcategories',
+                                        onClick: () => {
+                                            model.collapseSubCategories();
+                                        },
                                     },
+                                ]
+                                : []),
+                            {
+                                label: 'Collapse top-level categories',
+                                onClick: () => {
+                                    model.collapseTopLevelCategories();
                                 },
-                            ]
-                            : []),
-                        {
-                            label: 'Collapse top-level categories',
-                            onClick: () => {
-                                model.collapseTopLevelCategories();
                             },
-                        },
-                        {
-                            label: 'Expand all categories',
-                            onClick: () => {
-                                model.expandAllCategories();
+                            {
+                                label: 'Expand all categories',
+                                onClick: () => {
+                                    model.expandAllCategories();
+                                },
                             },
-                        },
-                    ],
-                },
-            ] },
-            react_1.default.createElement(Menu_1.default, null)),
-        react_1.default.createElement(react_1.Suspense, { fallback: null },
-            modalInfo ? (react_1.default.createElement(CloseConnectionDialog, { modalInfo: modalInfo, onClose: () => {
-                    setModalInfo(undefined);
-                } })) : null,
-            deleteDialogDetails ? (react_1.default.createElement(DeleteConnectionDialog, { handleClose: () => {
-                    setDeleteDialogDetails(undefined);
-                }, deleteDialogDetails: deleteDialogDetails, session: session })) : null,
-            connectionManagerOpen ? (react_1.default.createElement(ManageConnectionsDialog, { handleClose: () => {
-                    setConnectionManagerOpen(false);
-                }, breakConnection: breakConnection, session: session })) : null,
-            connectionToggleOpen ? (react_1.default.createElement(ToggleConnectionsDialog, { handleClose: () => {
-                    setConnectionToggleOpen(false);
-                }, session: session, breakConnection: breakConnection })) : null,
-            facetedOpen ? (react_1.default.createElement(FacetedDialog, { handleClose: () => {
-                    setFacetedOpen(false);
-                }, model: model })) : null)));
+                        ],
+                    },
+                ], children: (0, jsx_runtime_1.jsx)(Menu_1.default, {}) }), (0, jsx_runtime_1.jsxs)(react_1.Suspense, { fallback: null, children: [modalInfo ? ((0, jsx_runtime_1.jsx)(CloseConnectionDialog, { modalInfo: modalInfo, onClose: () => {
+                            setModalInfo(undefined);
+                        } })) : null, deleteDialogDetails ? ((0, jsx_runtime_1.jsx)(DeleteConnectionDialog, { handleClose: () => {
+                            setDeleteDialogDetails(undefined);
+                        }, deleteDialogDetails: deleteDialogDetails, session: session })) : null, connectionManagerOpen ? ((0, jsx_runtime_1.jsx)(ManageConnectionsDialog, { handleClose: () => {
+                            setConnectionManagerOpen(false);
+                        }, breakConnection: breakConnection, session: session })) : null, connectionToggleOpen ? ((0, jsx_runtime_1.jsx)(ToggleConnectionsDialog, { handleClose: () => {
+                            setConnectionToggleOpen(false);
+                        }, session: session, breakConnection: breakConnection })) : null, facetedOpen ? ((0, jsx_runtime_1.jsx)(FacetedDialog, { handleClose: () => {
+                            setFacetedOpen(false);
+                        }, model: model })) : null] })] }));
 });
 exports.default = HamburgerMenu;

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

@@ -1,7 +1,6 @@
-import React from 'react';
-import { HierarchicalTrackSelectorModel } from '../../model';
+import type { HierarchicalTrackSelectorModel } from '../../model';
 declare const HierarchicalTrackSelectorHeader: ({ model, setHeaderHeight, }: {
     model: HierarchicalTrackSelectorModel;
     setHeaderHeight: (n: number) => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HierarchicalTrackSelectorHeader;

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

@@ -3,12 +3,11 @@ 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 jsx_runtime_1 = require("react/jsx-runtime");
+const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
 const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const mobx_react_1 = require("mobx-react");
-// icons
-const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
+const mui_1 = require("tss-react/mui");
 const HamburgerMenu_1 = __importDefault(require("./HamburgerMenu"));
 const ShoppingCart_1 = __importDefault(require("../ShoppingCart"));
 const FavoriteTracks_1 = __importDefault(require("./FavoriteTracks"));
@@ -21,27 +20,19 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
 const SearchTracksTextField = (0, mobx_react_1.observer)(function ({ model, }) {
     const { filterText } = model;
     const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => {
+    return ((0, jsx_runtime_1.jsx)(material_1.TextField, { className: classes.searchBox, label: "Filter tracks", value: filterText, onChange: event => {
             model.setFilterText(event.target.value);
         }, fullWidth: true, slotProps: {
             input: {
-                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                endAdornment: ((0, jsx_runtime_1.jsx)(material_1.InputAdornment, { position: "end", children: (0, jsx_runtime_1.jsx)(material_1.IconButton, { onClick: () => {
                             model.clearFilterText();
-                        } },
-                        react_1.default.createElement(Clear_1.default, null)))),
+                        }, children: (0, jsx_runtime_1.jsx)(Clear_1.default, {}) }) })),
             },
         } }));
 });
 const HierarchicalTrackSelectorHeader = (0, mobx_react_1.observer)(function ({ model, setHeaderHeight, }) {
-    return (react_1.default.createElement("div", { ref: ref => {
+    return ((0, jsx_runtime_1.jsx)("div", { ref: ref => {
             setHeaderHeight((ref === null || ref === void 0 ? void 0 : ref.getBoundingClientRect().height) || 0);
-        }, "data-testid": "hierarchical_track_selector" },
-        react_1.default.createElement("div", { style: { display: 'flex' } },
-            react_1.default.createElement(HamburgerMenu_1.default, { model: model }),
-            react_1.default.createElement(ShoppingCart_1.default, { model: model }),
-            react_1.default.createElement(SearchTracksTextField, { model: model }),
-            react_1.default.createElement(RecentlyUsedTracks_1.default, { model: model }),
-            react_1.default.createElement(FavoriteTracks_1.default, { model: model }))));
+        }, "data-testid": "hierarchical_track_selector", children: (0, jsx_runtime_1.jsxs)("div", { style: { display: 'flex' }, children: [(0, jsx_runtime_1.jsx)(HamburgerMenu_1.default, { model: model }), (0, jsx_runtime_1.jsx)(ShoppingCart_1.default, { model: model }), (0, jsx_runtime_1.jsx)(SearchTracksTextField, { model: model }), (0, jsx_runtime_1.jsx)(RecentlyUsedTracks_1.default, { model: model }), (0, jsx_runtime_1.jsx)(FavoriteTracks_1.default, { model: model })] }) }));
 });
 exports.default = HierarchicalTrackSelectorHeader;

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

@@ -1,9 +1,8 @@
-import React from 'react';
-import { TreeNode } from '../../generateHierarchy';
-import { HierarchicalTrackSelectorModel } from '../../model';
+import type { TreeNode } from '../../generateHierarchy';
+import type { HierarchicalTrackSelectorModel } from '../../model';
 declare const HierarchicalTree: ({ height, tree, model, }: {
     height: number;
     tree: TreeNode;
     model: HierarchicalTrackSelectorModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HierarchicalTree;

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

@@ -1,35 +1,13 @@
 "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 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const react_vtree_1 = require("react-vtree");
-const util_1 = require("@jbrowse/core/util");
 const TrackListNode_1 = __importDefault(require("./TrackListNode"));
 function getNodeData(node, nestingLevel, extra, selection) {
     const isLeaf = node.type === 'track';
@@ -48,9 +26,6 @@ function getNodeData(node, nestingLevel, extra, selection) {
         node,
     };
 }
-// 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
 const HierarchicalTree = (0, mobx_react_1.observer)(function HierarchicalTree({ height, tree, model, }) {
     const { filterText, selection, view } = model;
     const treeRef = (0, react_1.useRef)(null);
@@ -71,33 +46,23 @@ const HierarchicalTree = (0, mobx_react_1.observer)(function HierarchicalTree({
         model,
         drawerPosition,
     }), [view, model, drawerPosition, tree]);
-    // doing this properly without ts-expect-error is tricky, react-vtree has
-    // some typescript examples that could help
-    const treeWalker = (0, react_1.useCallback)(
-    // @ts-expect-error
-    function* treeWalker() {
+    const treeWalker = (0, react_1.useCallback)(function* treeWalker() {
         for (const child of tree.children) {
             yield getNodeData(child, 0, extra, obj);
         }
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         while (true) {
-            // @ts-expect-error
             const parentMeta = yield;
-            // @ts-expect-error
             for (const curr of parentMeta.node.children) {
                 yield getNodeData(curr, parentMeta.nestingLevel + 1, extra, obj);
             }
         }
     }, [tree, extra, obj]);
-    /* biome-ignore lint/correctness/useExhaustiveDependencies: */
     (0, react_1.useEffect)(() => {
-        // @ts-expect-error
         treeRef.current.recomputeTree({
             refreshNodes: true,
             useDefaultHeight: true,
         });
     }, [tree, filterText]);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(react_vtree_1.VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, TrackListNode_1.default)));
+    return ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: (0, jsx_runtime_1.jsx)(react_vtree_1.VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height, children: TrackListNode_1.default }) }));
 });
 exports.default = HierarchicalTree;

package/dist/HierarchicalTrackSelectorWidget/components/tree/RecentlyUsedTracks.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { HierarchicalTrackSelectorModel } from '../../model';
+import type { HierarchicalTrackSelectorModel } from '../../model';
 declare const RecentlyUsedTracks: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default RecentlyUsedTracks;

package/dist/HierarchicalTrackSelectorWidget/components/tree/RecentlyUsedTracks.js

@@ -3,13 +3,12 @@ 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 jsx_runtime_1 = require("react/jsx-runtime");
+const History_1 = __importDefault(require("@mui/icons-material/History"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-// icons
-const History_1 = __importDefault(require("@mui/icons-material/History"));
-const DropdownTrackSelector_1 = __importDefault(require("./DropdownTrackSelector"));
 const mui_1 = require("tss-react/mui");
+const DropdownTrackSelector_1 = __importDefault(require("./DropdownTrackSelector"));
 const useStyles = (0, mui_1.makeStyles)()({
     smallBadge: {
         height: 14,
@@ -18,7 +17,7 @@ const useStyles = (0, mui_1.makeStyles)()({
 const RecentlyUsedTracks = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { view, recentlyUsedCounter, recentlyUsedTracks } = model;
-    return view ? (react_1.default.createElement(DropdownTrackSelector_1.default, { onClick: () => {
+    return view ? ((0, jsx_runtime_1.jsx)(DropdownTrackSelector_1.default, { onClick: () => {
             model.setRecentlyUsedCounter(0);
         }, model: model, tracks: recentlyUsedTracks, extraMenuItems: recentlyUsedTracks.length
             ? [
@@ -35,12 +34,9 @@ const RecentlyUsedTracks = (0, mobx_react_1.observer)(function ({ model, }) {
                     label: 'No recently used',
                     onClick: () => { },
                 },
-            ] },
-        react_1.default.createElement(material_1.Tooltip, { title: "Recently used tracks" },
-            react_1.default.createElement(material_1.Badge, { classes: { badge: classes.smallBadge }, anchorOrigin: {
+            ], children: (0, jsx_runtime_1.jsx)(material_1.Tooltip, { title: "Recently used tracks", children: (0, jsx_runtime_1.jsx)(material_1.Badge, { classes: { badge: classes.smallBadge }, anchorOrigin: {
                     vertical: 'bottom',
                     horizontal: 'right',
-                }, color: "secondary", badgeContent: recentlyUsedCounter },
-                react_1.default.createElement(History_1.default, null))))) : null;
+                }, color: "secondary", badgeContent: recentlyUsedCounter, children: (0, jsx_runtime_1.jsx)(History_1.default, {}) }) }) })) : null;
 });
 exports.default = RecentlyUsedTracks;

package/dist/HierarchicalTrackSelectorWidget/components/tree/TrackCategory.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { NodeData } from '../util';
+import type { NodeData } from '../util';
 export default function Category({ isOpen, setOpen, data, }: {
     isOpen: boolean;
     setOpen: (arg: boolean) => void;
     data: NodeData;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;