@jbrowse/plugin-data-management 2.10.3 → 2.11.0

package/dist/AddConnectionWidget/components/ConnectionTypeSelect.d.ts

@@ -2,7 +2,7 @@ import React from 'react';
 import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
     connectionTypeChoices: ConnectionType[];
-    connectionType?: ConnectionType | undefined;
+    connectionType?: ConnectionType;
     setConnectionType: (c?: ConnectionType) => void;
 }) => React.JSX.Element;
 export default ConnectionTypeSelect;

package/dist/AssemblyManager/AssemblyEditor.d.ts

@@ -1,10 +1,6 @@
 import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AssemblyEditor: ({ assembly, }: {
-    assembly?: ({
-        [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>) | undefined;
+    assembly?: AnyConfigurationModel;
 }) => React.JSX.Element;
 export default AssemblyEditor;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.d.ts

@@ -2,5 +2,5 @@ import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../model';
 declare const HierarchicalFab: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
-}) => React.JSX.Element;
+}) => React.JSX.Element | null;
 export default HierarchicalFab;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js

@@ -49,7 +49,7 @@ const HierarchicalFab = (0, mobx_react_1.observer)(function ({ model, }) {
     }
     const hasConnections = (0, util_1.isSessionModelWithConnections)(session);
     const hasAddTrack = (0, util_1.isSessionWithAddTracks)(session);
-    return (react_1.default.createElement(react_1.default.Fragment, null, hasAddTrack || hasConnections ? (react_1.default.createElement(react_1.default.Fragment, null,
+    return hasAddTrack || hasConnections ? (react_1.default.createElement(react_1.default.Fragment, null,
         react_1.default.createElement(material_1.Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
             react_1.default.createElement(Add_1.default, null)),
         react_1.default.createElement(material_1.Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) },
@@ -66,6 +66,6 @@ const HierarchicalFab = (0, mobx_react_1.observer)(function ({ model, }) {
                             view: model.view.id,
                         }));
                     }
-                } }, "Add track")) : null))) : null));
+                } }, "Add track")) : null))) : null;
 });
 exports.default = HierarchicalFab;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts

@@ -6,6 +6,6 @@ declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overr
     overrideDimensions?: {
         width: number;
         height: number;
-    } | undefined;
+    };
 }) => React.JSX.Element;
 export default HierarchicalTrackSelectorContainer;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js

@@ -38,7 +38,7 @@ const AutoSizedHierarchicalTree = ({ tree, model, offset, }) => {
     return typeof jest === 'undefined' ? (react_1.default.createElement(react_virtualized_auto_sizer_1.default, { disableWidth: true }, args => (react_1.default.createElement(HierarchicalTree_1.default, { height: (args.height || offset) - offset, model: model, tree: tree })))) : (react_1.default.createElement(HierarchicalTree_1.default, { height: 9000, model: model, tree: tree }));
 };
 const Wrapper = ({ overrideDimensions, children, }) => {
-    return overrideDimensions ? (react_1.default.createElement("div", { style: { ...overrideDimensions } }, children)) : (react_1.default.createElement(react_1.default.Fragment, null, children));
+    return overrideDimensions ? (react_1.default.createElement("div", { style: { ...overrideDimensions } }, children)) : (children);
 };
 const HierarchicalTrackSelectorContainer = (0, mobx_react_1.observer)(function ({ model, toolbarHeight, overrideDimensions, }) {
     return (react_1.default.createElement(Wrapper, { overrideDimensions: overrideDimensions },

package/dist/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.d.ts

@@ -1,10 +1,10 @@
 import React from 'react';
 declare const CloseConnectionDialog: ({ modalInfo, onClose, }: {
     modalInfo?: {
-        name?: string | undefined;
-        dereferenceTypeCount?: Record<string, number> | undefined;
-        safelyBreakConnection?: (() => void) | undefined;
-    } | undefined;
+        name?: string;
+        dereferenceTypeCount?: Record<string, number>;
+        safelyBreakConnection?: () => void;
+    };
     onClose: () => void;
 }) => React.JSX.Element;
 export default CloseConnectionDialog;

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

@@ -43,7 +43,7 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
         {
             field: 'name',
             hideable: false,
-            renderCell: (params) => {
+            renderCell: params => {
                 const { value, row } = params;
                 const { id, conf } = row;
                 return (react_1.default.createElement("div", { className: classes.cell },
@@ -54,29 +54,29 @@ const FacetedSelector = (0, mobx_react_1.observer)(function FacetedSelector({ mo
         },
         ...filteredNonMetadataKeys.map(e => {
             var _a;
-            return ({
+            return {
                 field: e,
                 width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
-                renderCell: (params) => {
+                renderCell: params => {
                     const val = params.value;
-                    return val ? react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val }) : '';
+                    return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
                 },
-            });
+            };
         }),
         ...filteredMetadataKeys.map(e => {
             var _a;
-            return ({
+            return {
                 field: `metadata.${e}`,
                 headerName: ['name', ...filteredNonMetadataKeys].includes(e)
                     ? `${e} (from metadata)`
                     : e,
                 width: (_a = widthsDebounced['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
-                valueGetter: (params) => params.row.metadata[e],
-                renderCell: (params) => {
-                    const val = params.row.metadata[e];
-                    return val ? react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val }) : '';
+                valueGetter: (_, row) => `${row.metadata[e]}`,
+                renderCell: params => {
+                    const val = params.value;
+                    return val ? (react_1.default.createElement(SanitizedHTML_1.default, { className: classes.cell, html: val })) : ('');
                 },
-            });
+            };
         }),
     ];
     return (react_1.default.createElement(react_1.default.Fragment, null,

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

@@ -6,7 +6,7 @@ declare const DropdownTrackSelector: ({ model, tracks, extraMenuItems, children,
     model: HierarchicalTrackSelectorModel;
     tracks: AnyConfigurationModel[];
     extraMenuItems: MenuItem[];
-    onClick?: (() => void) | undefined;
+    onClick?: () => void;
     children: React.ReactElement;
 }) => React.JSX.Element | null;
 export default DropdownTrackSelector;

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

@@ -4,9 +4,9 @@ import { HierarchicalTrackSelectorModel } from '../../model';
 declare const TrackLabelMenu: ({ id, trackId, stopPropagation, model, setOpen, conf, }: {
     id: string;
     trackId: string;
-    stopPropagation?: boolean | undefined;
+    stopPropagation?: boolean;
     conf: AnyConfigurationModel;
-    setOpen?: ((arg: boolean) => void) | undefined;
+    setOpen?: (arg: boolean) => void;
     model: HierarchicalTrackSelectorModel;
 }) => React.JSX.Element;
 export default TrackLabelMenu;

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -45,13 +45,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         visible: Record<string, boolean>;
-        widths: Record<string, number | undefined>; /**
-         * #property
-         */
+        widths: Record<string, number | undefined>;
         useShoppingCart: boolean;
-        filters: import("mobx").ObservableMap<string, string[]>; /**
-         * #property
-         */
+        filters: import("mobx").ObservableMap<string, string[]>;
     } & {
         setFilter(key: string, value: string[]): void;
         setPanelWidth(width: number): void;

package/dist/HierarchicalTrackSelectorWidget/model.js

@@ -12,13 +12,13 @@ const util_2 = require("./util");
 const facetedModel_1 = require("./facetedModel");
 // for settings that are config dependent
 function postNoConfigF() {
-    return typeof window !== undefined
+    return typeof window !== 'undefined'
         ? [window.location.host, window.location.pathname].join('-')
         : 'empty';
 }
 // for settings that are not config dependent
 function postF() {
-    return typeof window !== undefined
+    return typeof window !== 'undefined'
         ? [
             postNoConfigF(),
             new URLSearchParams(window.location.search).get('config'),
@@ -331,7 +331,7 @@ function stateTreeFactory(pluginManager) {
             const { connectionInstances = [] } = (0, util_1.getSession)(self);
             return [
                 ...this.configAndSessionTrackConfigurations,
-                ...connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks),
+                ...((connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks)) || []),
             ];
         },
         /**

package/dist/ucsc-trackhub/doConnect.js

@@ -124,7 +124,7 @@ async function doConnect(self) {
     }
     catch (e) {
         console.error(e);
-        session.notify(`${(0, configuration_1.getConf)(self, 'name')}: "${e}"`, 'error');
+        session.notifyError(`${(0, configuration_1.getConf)(self, 'name')}: "${e}"`, e);
         (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
     }
 }

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts

@@ -2,7 +2,7 @@ import React from 'react';
 import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
     connectionTypeChoices: ConnectionType[];
-    connectionType?: ConnectionType | undefined;
+    connectionType?: ConnectionType;
     setConnectionType: (c?: ConnectionType) => void;
 }) => React.JSX.Element;
 export default ConnectionTypeSelect;

package/esm/AssemblyManager/AssemblyEditor.d.ts

@@ -1,10 +1,6 @@
 import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AssemblyEditor: ({ assembly, }: {
-    assembly?: ({
-        [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>) | undefined;
+    assembly?: AnyConfigurationModel;
 }) => React.JSX.Element;
 export default AssemblyEditor;

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

@@ -2,5 +2,5 @@ import React from 'react';
 import { HierarchicalTrackSelectorModel } from '../model';
 declare const HierarchicalFab: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
-}) => React.JSX.Element;
+}) => React.JSX.Element | null;
 export default HierarchicalFab;

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js

@@ -21,7 +21,7 @@ const HierarchicalFab = observer(function ({ model, }) {
     }
     const hasConnections = isSessionModelWithConnections(session);
     const hasAddTrack = isSessionWithAddTracks(session);
-    return (React.createElement(React.Fragment, null, hasAddTrack || hasConnections ? (React.createElement(React.Fragment, null,
+    return hasAddTrack || hasConnections ? (React.createElement(React.Fragment, null,
         React.createElement(Fab, { color: "secondary", className: classes.fab, onClick: event => setAnchorEl(event.currentTarget) },
             React.createElement(AddIcon, null)),
         React.createElement(Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => setAnchorEl(null) },
@@ -38,6 +38,6 @@ const HierarchicalFab = observer(function ({ model, }) {
                             view: model.view.id,
                         }));
                     }
-                } }, "Add track")) : null))) : null));
+                } }, "Add track")) : null))) : null;
 });
 export default HierarchicalFab;

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

@@ -6,6 +6,6 @@ declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overr
     overrideDimensions?: {
         width: number;
         height: number;
-    } | undefined;
+    };
 }) => React.JSX.Element;
 export default HierarchicalTrackSelectorContainer;

package/esm/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.js

@@ -10,7 +10,7 @@ const AutoSizedHierarchicalTree = ({ tree, model, offset, }) => {
     return typeof jest === 'undefined' ? (React.createElement(AutoSizer, { disableWidth: true }, args => (React.createElement(HierarchicalTree, { height: (args.height || offset) - offset, model: model, tree: tree })))) : (React.createElement(HierarchicalTree, { height: 9000, model: model, tree: tree }));
 };
 const Wrapper = ({ overrideDimensions, children, }) => {
-    return overrideDimensions ? (React.createElement("div", { style: { ...overrideDimensions } }, children)) : (React.createElement(React.Fragment, null, children));
+    return overrideDimensions ? (React.createElement("div", { style: { ...overrideDimensions } }, children)) : (children);
 };
 const HierarchicalTrackSelectorContainer = observer(function ({ model, toolbarHeight, overrideDimensions, }) {
     return (React.createElement(Wrapper, { overrideDimensions: overrideDimensions },

package/esm/HierarchicalTrackSelectorWidget/components/dialogs/CloseConnectionDialog.d.ts

@@ -1,10 +1,10 @@
 import React from 'react';
 declare const CloseConnectionDialog: ({ modalInfo, onClose, }: {
     modalInfo?: {
-        name?: string | undefined;
-        dereferenceTypeCount?: Record<string, number> | undefined;
-        safelyBreakConnection?: (() => void) | undefined;
-    } | undefined;
+        name?: string;
+        dereferenceTypeCount?: Record<string, number>;
+        safelyBreakConnection?: () => void;
+    };
     onClose: () => void;
 }) => React.JSX.Element;
 export default CloseConnectionDialog;

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

@@ -38,7 +38,7 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
         {
             field: 'name',
             hideable: false,
-            renderCell: (params) => {
+            renderCell: params => {
                 const { value, row } = params;
                 const { id, conf } = row;
                 return (React.createElement("div", { className: classes.cell },
@@ -49,29 +49,29 @@ const FacetedSelector = observer(function FacetedSelector({ model, }) {
         },
         ...filteredNonMetadataKeys.map(e => {
             var _a;
-            return ({
+            return {
                 field: e,
                 width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
-                renderCell: (params) => {
+                renderCell: params => {
                     const val = params.value;
-                    return val ? React.createElement(SanitizedHTML, { className: classes.cell, html: val }) : '';
+                    return val ? (React.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
                 },
-            });
+            };
         }),
         ...filteredMetadataKeys.map(e => {
             var _a;
-            return ({
+            return {
                 field: `metadata.${e}`,
                 headerName: ['name', ...filteredNonMetadataKeys].includes(e)
                     ? `${e} (from metadata)`
                     : e,
                 width: (_a = widthsDebounced['metadata.' + e]) !== null && _a !== void 0 ? _a : 100,
-                valueGetter: (params) => params.row.metadata[e],
-                renderCell: (params) => {
-                    const val = params.row.metadata[e];
-                    return val ? React.createElement(SanitizedHTML, { className: classes.cell, html: val }) : '';
+                valueGetter: (_, row) => `${row.metadata[e]}`,
+                renderCell: params => {
+                    const val = params.value;
+                    return val ? (React.createElement(SanitizedHTML, { className: classes.cell, html: val })) : ('');
                 },
-            });
+            };
         }),
     ];
     return (React.createElement(React.Fragment, null,

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

@@ -6,7 +6,7 @@ declare const DropdownTrackSelector: ({ model, tracks, extraMenuItems, children,
     model: HierarchicalTrackSelectorModel;
     tracks: AnyConfigurationModel[];
     extraMenuItems: MenuItem[];
-    onClick?: (() => void) | undefined;
+    onClick?: () => void;
     children: React.ReactElement;
 }) => React.JSX.Element | null;
 export default DropdownTrackSelector;

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

@@ -4,9 +4,9 @@ import { HierarchicalTrackSelectorModel } from '../../model';
 declare const TrackLabelMenu: ({ id, trackId, stopPropagation, model, setOpen, conf, }: {
     id: string;
     trackId: string;
-    stopPropagation?: boolean | undefined;
+    stopPropagation?: boolean;
     conf: AnyConfigurationModel;
-    setOpen?: ((arg: boolean) => void) | undefined;
+    setOpen?: (arg: boolean) => void;
     model: HierarchicalTrackSelectorModel;
 }) => React.JSX.Element;
 export default TrackLabelMenu;

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -45,13 +45,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
     }, {
         visible: Record<string, boolean>;
-        widths: Record<string, number | undefined>; /**
-         * #property
-         */
+        widths: Record<string, number | undefined>;
         useShoppingCart: boolean;
-        filters: import("mobx").ObservableMap<string, string[]>; /**
-         * #property
-         */
+        filters: import("mobx").ObservableMap<string, string[]>;
     } & {
         setFilter(key: string, value: string[]): void;
         setPanelWidth(width: number): void;

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -10,13 +10,13 @@ import { findSubCategories, findTopLevelCategories } from './util';
 import { facetedStateTreeF } from './facetedModel';
 // for settings that are config dependent
 function postNoConfigF() {
-    return typeof window !== undefined
+    return typeof window !== 'undefined'
         ? [window.location.host, window.location.pathname].join('-')
         : 'empty';
 }
 // for settings that are not config dependent
 function postF() {
-    return typeof window !== undefined
+    return typeof window !== 'undefined'
         ? [
             postNoConfigF(),
             new URLSearchParams(window.location.search).get('config'),
@@ -329,7 +329,7 @@ export default function stateTreeFactory(pluginManager) {
             const { connectionInstances = [] } = getSession(self);
             return [
                 ...this.configAndSessionTrackConfigurations,
-                ...connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks),
+                ...((connectionInstances === null || connectionInstances === void 0 ? void 0 : connectionInstances.flatMap(c => c.tracks)) || []),
             ];
         },
         /**

package/esm/ucsc-trackhub/doConnect.js

@@ -121,7 +121,7 @@ export async function doConnect(self) {
     }
     catch (e) {
         console.error(e);
-        session.notify(`${getConf(self, 'name')}: "${e}"`, 'error');
+        session.notifyError(`${getConf(self, 'name')}: "${e}"`, e);
         (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.10.3",
+  "version": "2.11.0",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -38,7 +38,7 @@
   "dependencies": {
     "@gmod/ucsc-hub": "^0.3.0",
     "@mui/icons-material": "^5.0.1",
-    "@mui/x-data-grid": "^6.0.1",
+    "@mui/x-data-grid": "^7.0.0",
     "react-virtualized-auto-sizer": "^1.0.2",
     "react-vtree": "^3.0.0-beta.1",
     "react-window": "^1.8.6"
@@ -60,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c8fc800cd17decd72b2e971c7a6add3b95214e72"
+  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
 }