@jbrowse/plugin-data-management 2.5.0 → 2.6.2

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

@@ -22,8 +22,8 @@ import { getRootKeys } from './util';
 const nonMetadataKeys = ['category', 'adapter', 'description'];
 const frac = 0.75;
 export default observer(function FacetedSelector({ model, }) {
-    var _a;
-    const { assemblyNames, view, selection } = model;
+    var _a, _b;
+    const { view, selection } = model;
     const { pluginManager } = getEnv(model);
     const { ref, scrollLeft } = useResizeBar();
     const [filterText, setFilterText] = useState('');
@@ -32,17 +32,16 @@ export default observer(function FacetedSelector({ model, }) {
     const [useShoppingCart, setUseShoppingCart] = useState(false);
     const [hideSparse, setHideSparse] = useState(true);
     const [panelWidth, setPanelWidth] = useState(400);
-    const assemblyName = assemblyNames[0];
     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 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)
-        return model
-            .trackConfigurations(assemblyName)
+        return model.trackConfigurations
             .filter(conf => matches(filterDebounced, conf, session))
             .map(track => {
             var _a, _b;
@@ -58,14 +57,12 @@ export default observer(function FacetedSelector({ model, }) {
                 ...metadata,
             };
         });
-    }, [assemblyName, model, filterDebounced, session]);
+    }, [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
         ? true
         : rows.map(r => r.metadata[f]).filter(f => !!f).length > 5), [hideSparse, rows]);
-    const fields = useMemo(() => {
-        return ['name', ...filteredNonMetadataKeys, ...filteredMetadataKeys];
-    }, [filteredNonMetadataKeys, filteredMetadataKeys]);
+    const fields = useMemo(() => ['name', ...filteredNonMetadataKeys, ...filteredMetadataKeys], [filteredNonMetadataKeys, filteredMetadataKeys]);
     const [widths, setWidths] = useState({
         name: measureGridWidth(rows.map(r => r.name), { maxWidth: 500, stripHTML: true }) + 15,
         ...Object.fromEntries(filteredNonMetadataKeys.map(e => [
@@ -117,31 +114,35 @@ export default observer(function FacetedSelector({ model, }) {
                         }) },
                         React.createElement(MoreHoriz, null))));
             },
-            width: widthsDebounced.name || 100, // can be undefined before useEffect update
+            width: (_a = widthsDebounced.name) !== null && _a !== void 0 ? _a : 100,
         },
-        ...filteredNonMetadataKeys.map(e => ({
-            field: e,
-            width: widthsDebounced[e] || 100,
-            renderCell: (params) => {
-                const { value } = params;
-                return value ? React.createElement(SanitizedHTML, { html: value }) : '';
-            },
-        })),
-        ...filteredMetadataKeys.map(e => ({
-            field: e,
-            width: widthsDebounced[e] || 100,
-            renderCell: (params) => {
-                const { value } = params;
-                return value ? React.createElement(SanitizedHTML, { html: value }) : '';
-            },
-        })),
+        ...filteredNonMetadataKeys.map(e => {
+            var _a;
+            return ({
+                field: e,
+                width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
+                renderCell: (params) => {
+                    const { value } = params;
+                    return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+                },
+            });
+        }),
+        ...filteredMetadataKeys.map(e => {
+            var _a;
+            return ({
+                field: e,
+                width: (_a = widthsDebounced[e]) !== null && _a !== void 0 ? _a : 100,
+                renderCell: (params) => {
+                    const { value } = params;
+                    return value ? React.createElement(SanitizedHTML, { html: value }) : '';
+                },
+            });
+        }),
     ];
-    const shownTrackIds = view.tracks.map(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    (t) => t.configuration.trackId);
+    const shownTrackIds = tracks.map(t => t.configuration.trackId);
     const arrFilters = Object.entries(filters).filter(f => f[1].length > 0);
     return (React.createElement(React.Fragment, null,
-        info ? (React.createElement(JBrowseMenu, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: ((_a = session.getTrackActionMenuItems) === null || _a === void 0 ? void 0 : _a.call(session, info.conf)) || [], onMenuItemClick: (_event, callback) => {
+        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,
@@ -156,7 +157,7 @@ export default observer(function FacetedSelector({ model, }) {
                     height: window.innerHeight * frac,
                     width: window.innerWidth * frac - panelWidth,
                 } },
-                React.createElement(ResizeBar, { checkbox: true, widths: Object.values(widths), setWidths: newWidths => setWidths(Object.fromEntries(Object.entries(widths).map((entry, idx) => [
+                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 }),
@@ -184,4 +185,3 @@ export default observer(function FacetedSelector({ model, }) {
             React.createElement("div", { style: { width: panelWidth, overflowY: 'auto', overflowX: 'hidden' } },
                 React.createElement(FacetFilters, { width: panelWidth - 10, rows: rows, columns: columns, dispatch: dispatch, filters: filters })))));
 });
-//# sourceMappingURL=FacetedSelector.js.map

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

@@ -3,4 +3,3 @@ export function getRootKeys(obj) {
         .map(([key, val]) => (typeof val === 'string' ? key : ''))
         .filter(f => !!f);
 }
-//# sourceMappingURL=util.js.map

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

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

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

@@ -3,7 +3,7 @@ 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, isSessionModelWithWidgets, isSessionModelWithConnections, } from '@jbrowse/core/util';
+import { getSession, isSessionModelWithConnectionEditing, isSessionModelWithConnections, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
 import { readConfObject, } from '@jbrowse/core/configuration';
 // icons
 import MenuIcon from '@mui/icons-material/Menu';
@@ -18,7 +18,7 @@ const useStyles = makeStyles()(theme => ({
         marginBottom: 0,
     },
 }));
-export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
+export default observer(function HamburgerMenu({ model, }) {
     const session = getSession(model);
     const [menuEl, setMenuEl] = useState();
     const [modalInfo, setModalInfo] = useState();
@@ -26,7 +26,6 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
     const [connectionToggleOpen, setConnectionToggleOpen] = useState(false);
     const [connectionManagerOpen, setConnectionManagerOpen] = useState(false);
     const { classes } = useStyles();
-    const { assemblyNames } = model;
     function breakConnection(connectionConf, deletingConnection) {
         const name = readConfObject(connectionConf, 'name');
         const result = session.prepareToBreakConnection(connectionConf);
@@ -48,26 +47,6 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
             setDeleteDlgDetails({ name, connectionConf });
         }
     }
-    const connectionMenuItems = [
-        {
-            label: 'Turn on/off connections...',
-            onClick: () => setConnectionToggleOpen(true),
-        },
-    ];
-    if (isSessionModelWithConnections(session)) {
-        connectionMenuItems.unshift({
-            label: 'Add connection...',
-            onClick: () => {
-                if (isSessionModelWithWidgets(session)) {
-                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
-                }
-            },
-        });
-        connectionMenuItems.push({
-            label: 'Delete connections...',
-            onClick: () => setConnectionManagerOpen(true),
-        });
-    }
     return (React.createElement(React.Fragment, null,
         React.createElement(IconButton, { className: classes.menuIcon, onClick: event => setMenuEl(event.currentTarget) },
             React.createElement(MenuIcon, null)),
@@ -75,33 +54,48 @@ export default observer(function HamburgerMenu({ model, setAssemblyIdx, }) {
                 callback();
                 setMenuEl(undefined);
             }, onClose: () => setMenuEl(undefined), menuItems: [
-                {
-                    label: 'Add track...',
-                    onClick: () => {
-                        if (isSessionModelWithWidgets(session)) {
-                            session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
-                                view: model.view.id,
-                            }));
-                        }
-                    },
-                },
-                ...(session.makeConnection ? connectionMenuItems : []),
-                ...(assemblyNames.length > 1
+                ...(isSessionWithAddTracks(session)
                     ? [
                         {
-                            label: 'Select assembly...',
-                            subMenu: assemblyNames.map((name, idx) => ({
-                                label: name,
-                                onClick: () => setAssemblyIdx(idx),
-                            })),
+                            label: 'Add track...',
+                            onClick: () => {
+                                if (isSessionModelWithWidgets(session)) {
+                                    session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                        view: model.view.id,
+                                    }));
+                                }
+                            },
+                        },
+                    ]
+                    : []),
+                ...(isSessionModelWithConnections(session)
+                    ? [
+                        {
+                            label: 'Turn on/off connections...',
+                            onClick: () => setConnectionToggleOpen(true),
+                        },
+                    ]
+                    : []),
+                ...(isSessionModelWithConnectionEditing(session)
+                    ? [
+                        {
+                            label: 'Add connection...',
+                            onClick: () => {
+                                if (isSessionModelWithWidgets(session)) {
+                                    session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                                }
+                            },
+                        },
+                        {
+                            label: 'Delete connections...',
+                            onClick: () => setConnectionManagerOpen(true),
                         },
                     ]
                     : []),
             ] }),
-        React.createElement(Suspense, { fallback: React.createElement("div", null) },
-            modalInfo ? (React.createElement(CloseConnectionDlg, { modalInfo: modalInfo, setModalInfo: setModalInfo })) : 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)));
 });
-//# sourceMappingURL=HamburgerMenu.js.map

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

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

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

@@ -17,13 +17,13 @@ const useStyles = makeStyles()(theme => ({
         marginBottom: 0,
     },
 }));
-function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyIdx, }) {
+function HierarchicalTrackSelectorHeader({ 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, setAssemblyIdx: setAssemblyIdx }),
+            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" },
@@ -34,4 +34,3 @@ function HierarchicalTrackSelectorHeader({ model, setHeaderHeight, setAssemblyId
         React.createElement(Suspense, { fallback: React.createElement("div", null) }, facetedOpen ? (React.createElement(FacetedDialog, { handleClose: () => setFacetedOpen(false), model: model })) : null)));
 }
 export default observer(HierarchicalTrackSelectorHeader);
-//# sourceMappingURL=HierarchicalHeader.js.map

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

@@ -1,7 +1,8 @@
+import React from 'react';
 import { TreeNode, HierarchicalTrackSelectorModel } from '../../model';
 declare const _default: ({ height, tree, model, }: {
     height: number;
     tree: TreeNode;
     model: HierarchicalTrackSelectorModel;
-}) => JSX.Element;
+}) => React.JSX.Element;
 export default _default;

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

@@ -60,4 +60,3 @@ export default observer(function HierarchicalTree({ height, tree, model, }) {
     return (React.createElement(React.Fragment, null,
         React.createElement(VariableSizeTree, { ref: treeRef, treeWalker: treeWalker, height: height }, Node)));
 });
-//# sourceMappingURL=HierarchicalTree.js.map

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

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

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

@@ -57,4 +57,3 @@ export default function Category({ isOpen, setOpen, data, }) {
                 setMenuEl(null);
             }, open: Boolean(menuEl), onClose: () => setMenuEl(null) })) : null));
 }
-//# sourceMappingURL=TrackCategory.js.map

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

@@ -1,3 +1,4 @@
+import React from 'react';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { NodeData } from '../util';
 export interface InfoArgs {
@@ -7,4 +8,4 @@ export interface InfoArgs {
 }
 export default function TrackLabel({ data }: {
     data: NodeData;
-}): JSX.Element;
+}): React.JSX.Element;

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

@@ -54,4 +54,3 @@ export default function TrackLabel({ data }) {
                 setInfo(undefined);
             }, open: Boolean(info), onClose: () => setInfo(undefined) })) : null));
 }
-//# sourceMappingURL=TrackLabel.js.map

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

@@ -1,3 +1,4 @@
+import React from 'react';
 import { NodeData } from '../util';
 export default function Node({ data, isOpen, style, setOpen, }: {
     data: NodeData;
@@ -6,4 +7,4 @@ export default function Node({ data, isOpen, style, setOpen, }: {
         height: number;
     };
     setOpen: (arg: boolean) => void;
-}): JSX.Element;
+}): React.JSX.Element;

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

@@ -45,4 +45,3 @@ export default function Node({ data, isOpen, style, setOpen, }) {
             } },
             React.createElement("div", { className: !isLeaf ? classes.accordionColor : undefined }, !isLeaf ? (React.createElement(Category, { isOpen: isOpen, data: data, setOpen: setOpen })) : (React.createElement(TrackLabel, { data: data }))))));
 }
-//# sourceMappingURL=TrackListNode.js.map

package/esm/HierarchicalTrackSelectorWidget/components/util.js

@@ -15,4 +15,3 @@ export function treeToMap(tree, map = new Map()) {
 export function isUnsupported(name = '') {
     return name.endsWith('(Unsupported)') || name.endsWith('(Unknown)');
 }
-//# sourceMappingURL=util.js.map

package/esm/HierarchicalTrackSelectorWidget/configSchema.js

@@ -1,4 +1,3 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 const configSchema = ConfigurationSchema('HierarchicalTrackSelectorWidget', {});
 export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/esm/HierarchicalTrackSelectorWidget/index.js

@@ -15,4 +15,3 @@ export default (pluginManager) => {
 };
 export { default as stateModelFactory, } from './model';
 export { default as configSchema } from './configSchema';
-//# sourceMappingURL=index.js.map

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -14,10 +14,25 @@ export type TreeNode = {
 export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
     get: (arg: string) => boolean | undefined;
 }, extra?: string): TreeNode[];
+/**
+ * #stateModel HierarchicalTrackSelectorWidget
+ */
 export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
+    /**
+     * #property
+     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+    /**
+     * #property
+     */
     type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
+    /**
+     * #property
+     */
     collapsed: import("mobx-state-tree").IMapType<import("mobx-state-tree").ISimpleType<boolean>>;
+    /**
+     * #property
+     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     selection: ({
@@ -27,28 +42,74 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     filterText: string;
 } & {
+    /**
+     * #action
+     */
     setSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     addToSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     removeFromSelection(elt: AnyConfigurationModel[]): void;
+    /**
+     * #action
+     */
     clearSelection(): void;
+    /**
+     * #action
+     */
     setView(view: unknown): void;
+    /**
+     * #action
+     */
     toggleCategory(pathName: string): void;
+    /**
+     * #action
+     */
     clearFilterText(): void;
+    /**
+     * #action
+     */
     setFilterText(newText: string): void;
 } & {
-    getRefSeqTrackConf(assemblyName: string): any;
+    /**
+     * #method
+     */
+    getRefSeqTrackConf(assemblyName: string): AnyConfigurationModel | undefined;
 } & {
-    trackConfigurations(assemblyName: string): any[];
+    /**
+     * #getter
+     */
     readonly assemblyNames: string[];
-    connectionTrackConfigurations(assemblyName: string, connection: {
+} & {
+    /**
+     * #method
+     * filter out tracks that don't match the current display types
+     */
+    connectionTrackConfigurations(connection: {
         tracks: AnyConfigurationModel[];
     }): ({
         [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>)[];
+    /**
+     * #getter
+     * filter out tracks that don't match the current assembly/display types
+     */
+    readonly trackConfigurations: ({
+        [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>)[];
 } & {
-    hierarchy(assemblyName: string): {
+    /**
+     * #getter
+     */
+    readonly hierarchy: {
         name: string;
         id: string;
         children: ({
@@ -64,7 +125,10 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             children: TreeNode[];
         })[];
     };
-    connectionHierarchy(assemblyName: string, connection: {
+    /**
+     * #method
+     */
+    connectionHierarchy(connection: {
         name: string;
         tracks: AnyConfigurationModel[];
     }): TreeNode[];