@jbrowse/plugin-data-management 2.6.2 → 2.7.0

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

@@ -51,7 +51,7 @@ 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
-exports.default = (0, mobx_react_1.observer)(function HierarchicalTree({ height, tree, model, }) {
+const HierarchicalTree = (0, mobx_react_1.observer)(function HierarchicalTree({ height, tree, model, }) {
     const { filterText, selection, view } = model;
     const treeRef = (0, react_1.useRef)(null);
     const session = (0, util_1.getSession)(model);
@@ -65,15 +65,13 @@ exports.default = (0, mobx_react_1.observer)(function HierarchicalTree({ height,
         drawerPosition,
     }), [view, model, drawerPosition, tree]);
     const treeWalker = (0, react_1.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);
             }
         }
@@ -88,3 +86,4 @@ exports.default = (0, mobx_react_1.observer)(function HierarchicalTree({ height,
     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)));
 });
+exports.default = HierarchicalTree;

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

@@ -80,6 +80,28 @@ function Category({ isOpen, setOpen, data, }) {
                         model.removeFromSelection((0, util_1.getAllChildren)(r));
                     },
                 },
+                {
+                    label: 'Show all tracks',
+                    onClick: () => {
+                        var _a;
+                        for (const entry of ((_a = (0, util_1.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 = (0, util_1.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/dist/HierarchicalTrackSelectorWidget/components/tree/TrackLabel.js

@@ -31,12 +31,12 @@ const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const Menu_1 = __importDefault(require("@jbrowse/core/ui/Menu"));
 const util_1 = require("@jbrowse/core/util");
+const SanitizedHTML_1 = __importDefault(require("@jbrowse/core/ui/SanitizedHTML"));
 const configuration_1 = require("@jbrowse/core/configuration");
 // icons
 const MoreHoriz_1 = __importDefault(require("@mui/icons-material/MoreHoriz"));
 // locals
 const util_2 = require("../util");
-const ui_1 = require("@jbrowse/core/ui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     compactCheckbox: {
         padding: 0,
@@ -59,8 +59,8 @@ function TrackLabel({ data }) {
             react_1.default.createElement(material_1.FormControlLabel, { className: classes.checkboxLabel, control: react_1.default.createElement(material_1.Checkbox, { className: classes.compactCheckbox, checked: checked, onChange: () => onChange(id), disabled: (0, util_2.isUnsupported)(name), inputProps: {
                         // @ts-expect-error
                         'data-testid': `htsTrackEntry-${id}`,
-                    } }), label: react_1.default.createElement("div", { style: { background: selected ? '#cccc' : undefined } },
-                    react_1.default.createElement(ui_1.SanitizedHTML, { html: name })) })),
+                    } }), label: react_1.default.createElement("div", { "data-testid": `htsTrackLabel-${id}`, style: { background: selected ? '#cccc' : undefined } },
+                    react_1.default.createElement(SanitizedHTML_1.default, { html: name })) })),
         react_1.default.createElement(material_1.IconButton, { onClick: e => setInfo({ target: e.currentTarget, id, conf }), style: { padding: 0 }, "data-testid": `htsTrackEntryMenu-${id}` },
             react_1.default.createElement(MoreHoriz_1.default, null)),
         info ? (react_1.default.createElement(Menu_1.default, { anchorEl: info === null || info === void 0 ? void 0 : info.target, menuItems: [

package/dist/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/dist/HierarchicalTrackSelectorWidget/components/util.js

@@ -10,8 +10,7 @@ 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/dist/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/dist/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -0,0 +1,32 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.filterTracks = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+function filterTracks(tracks, self) {
+    const { assemblyManager } = (0, util_1.getSession)(self);
+    const { pluginManager } = (0, util_1.getEnv)(self);
+    const { view } = self;
+    if (!view) {
+        return [];
+    }
+    const trackListAssemblies = self.assemblyNames
+        .map(a => assemblyManager.get(a))
+        .filter(util_1.notEmpty);
+    return tracks
+        .filter(c => {
+        const trackAssemblyNames = (0, configuration_1.readConfObject)(c, 'assemblyNames');
+        const trackAssemblies = trackAssemblyNames === null || trackAssemblyNames === void 0 ? void 0 : trackAssemblyNames.map(name => assemblyManager.get(name)).filter(util_1.notEmpty);
+        return view.trackSelectorAnyOverlap
+            ? (0, util_2.hasAnyOverlap)(trackAssemblies, trackListAssemblies)
+            : (0, util_2.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 (0, util_2.hasAnyOverlap)(compatDisplays, trackDisplays);
+    });
+}
+exports.filterTracks = filterTracks;

package/dist/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/dist/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -0,0 +1,98 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateHierarchy = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+// locals
+const util_2 = require("./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,
+            (0, configuration_1.readConfObject)(c, 'name'),
+            ((_a = (0, configuration_1.readConfObject)(c, 'category')) === null || _a === void 0 ? void 0 : _a[0]) || '',
+            ((_b = (0, configuration_1.readConfObject)(c, 'category')) === null || _b === void 0 ? void 0 : _b[1]) || '',
+            ((_c = (0, configuration_1.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]);
+}
+function generateHierarchy(model, trackConfs, collapsed, extra) {
+    const hierarchy = { children: [] };
+    const { filterText, activeSortTrackNames, activeSortCategories, view } = model;
+    if (!view) {
+        return [];
+    }
+    const session = (0, util_1.getSession)(model);
+    const viewTracks = view.tracks;
+    const confs = trackConfs.filter(conf => (0, util_2.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 = [...((0, configuration_1.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: (0, tracks_1.getTrackName)(conf, session),
+            conf,
+            checked: viewTracks.some(f => f.configuration === conf),
+            children: [],
+        });
+    }
+    return hierarchy.children;
+}
+exports.generateHierarchy = generateHierarchy;

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,19 +1,7 @@
 import { Instance } from 'mobx-state-tree';
 import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { AbstractSessionModel } from '@jbrowse/core/util';
 import PluginManager from '@jbrowse/core/PluginManager';
-export declare function matches(query: string, conf: AnyConfigurationModel, session: AbstractSessionModel): boolean;
-export type TreeNode = {
-    name: string;
-    id: string;
-    conf?: AnyConfigurationModel;
-    checked?: boolean;
-    isOpenByDefault?: boolean;
-    children: TreeNode[];
-};
-export declare function generateHierarchy(model: HierarchicalTrackSelectorModel, trackConfigurations: AnyConfigurationModel[], collapsed: {
-    get: (arg: string) => boolean | undefined;
-}, extra?: string): TreeNode[];
+import { TreeNode } from './generateHierarchy';
 /**
  * #stateModel HierarchicalTrackSelectorWidget
  */
@@ -26,10 +14,22 @@ 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
      */
@@ -42,6 +42,14 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
     filterText: string;
 } & {
+    /**
+     * #action
+     */
+    setSortTrackNames(val: boolean): void;
+    /**
+     * #action
+     */
+    setSortCategories(val: boolean): void;
     /**
      * #action
      */
@@ -66,6 +74,14 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      * #action
      */
     toggleCategory(pathName: string): void;
+    /**
+     * #action
+     */
+    setCategoryCollapsed(pathName: string, status: boolean): void;
+    /**
+     * #action
+     */
+    expandAllCategories(): void;
     /**
      * #action
      */
@@ -85,6 +101,14 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
      */
     readonly assemblyNames: string[];
 } & {
+    /**
+     * #getter
+     */
+    readonly activeSortTrackNames: any;
+    /**
+     * #getter
+     */
+    readonly activeSortCategories: any;
     /**
      * #method
      * filter out tracks that don't match the current display types
@@ -105,6 +129,23 @@ 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>)[];
+} & {
+    /**
+     * #method
+     */
+    connectionHierarchy(connection: {
+        name: string;
+        tracks: AnyConfigurationModel[];
+    }): TreeNode[];
+} & {
+    readonly allTracks: {
+        group: any;
+        tracks: ({
+            [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
@@ -112,26 +153,25 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
     readonly hierarchy: {
         name: string;
         id: string;
-        children: ({
-            id: any;
+        children: {
             name: any;
+            id: any;
             children: TreeNode[];
-            state: {
-                expanded: boolean;
-            };
-        } | {
-            name: string;
-            id: string;
-            children: TreeNode[];
-        })[];
+        }[];
     };
+} & {
     /**
-     * #method
+     * #action
      */
-    connectionHierarchy(connection: {
-        name: string;
-        tracks: AnyConfigurationModel[];
-    }): TreeNode[];
+    collapseSubCategories(): void;
+    /**
+     * #action
+     */
+    collapseTopLevelCategories(): void;
+} & {
+    afterCreate(): void;
+} & {
+    readonly hasAnySubcategories: boolean;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
 export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;