@jbrowse/plugin-data-management 2.10.3 → 2.11.1

package/dist/index.d.ts

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

package/dist/index.js

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

package/dist/ucsc-trackhub/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/dist/ucsc-trackhub/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function UCSCTrackHubConnectionF(pluginManager: PluginManager): void;

package/dist/ucsc-trackhub/index.js

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

package/esm/AddConnectionWidget/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/AddConnectionWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function AddConnectionWidgetF(pluginManager: PluginManager): void;

package/esm/AddConnectionWidget/index.js

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

package/esm/AddTrackWidget/index.d.ts

@@ -1,3 +1,2 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function AddTrackWidgetF(pluginManager: PluginManager): void;

package/esm/AddTrackWidget/index.js

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

package/esm/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/index.d.ts

@@ -1,5 +1,4 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const _default: (pluginManager: PluginManager) => void;
-export default _default;
+export default function HierarchicalTrackSelectorWidgetF(pluginManager: PluginManager): void;
 export { type HierarchicalTrackSelectorModel, default as stateModelFactory, } from './model';
 export { default as configSchema } from './configSchema';

package/esm/HierarchicalTrackSelectorWidget/index.js

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

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -14,22 +14,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #property
      */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
-    /**
-     * #property
-     */
-    initialized: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    sortTrackNames: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    /**
-     * #property
-     */
-    sortCategories: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     /**
      * #property
      */
@@ -45,13 +29,9 @@ 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;
@@ -111,6 +91,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: unknown): any;
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
+    sortTrackNames: boolean;
+    sortCategories: boolean;
+    collapsed: import("mobx").ObservableMap<string, boolean>;
     filterText: string;
     recentlyUsedCounter: number;
     favoritesCounter: number;
@@ -135,6 +118,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #getter
      */
     readonly recentlyUsedSet: Set<string>;
+    /**
+     * #getter
+     */
+    readonly assemblyNames: string[];
 } & {
     /**
      * #action
@@ -212,6 +199,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #action
      */
     expandAllCategories(): void;
+    /**
+     * #action
+     */
+    setCollapsedCategories(str: [string, boolean][]): void;
     /**
      * #action
      */
@@ -241,24 +232,11 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     /**
      * #getter
      */
-    readonly assemblyNames: string[];
-} & {
-    /**
-     * #getter
-     */
-    readonly recentlyUsedLocalStorageKey: string;
+    readonly activeSortTrackNames: boolean;
     /**
      * #getter
      */
-    readonly favoritesLocalStorageKey: string;
-    /**
-     * #getter
-     */
-    readonly activeSortTrackNames: any;
-    /**
-     * #getter
-     */
-    readonly activeSortCategories: any;
+    readonly activeSortCategories: boolean;
     /**
      * #getter
      * filter out tracks that don't match the current assembly/display types
@@ -344,8 +322,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #action
      */
     collapseTopLevelCategories(): void;
-} & {
-    afterCreate(): void;
 } & {
     /**
      * #getter