@jbrowse/plugin-data-management 2.11.0 → 2.11.2

package/esm/HierarchicalTrackSelectorWidget/model.js

@@ -1,5 +1,5 @@
 import { types, addDisposer } from 'mobx-state-tree';
-import { autorun } from 'mobx';
+import { autorun, observable } from 'mobx';
 import { getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { dedupe, getSession, localStorageGetItem, localStorageSetItem, notEmpty, } from '@jbrowse/core/util';
 import { ElementId } from '@jbrowse/core/util/types/mst';
@@ -8,21 +8,52 @@ import { filterTracks } from './filterTracks';
 import { generateHierarchy } from './generateHierarchy';
 import { findSubCategories, findTopLevelCategories } from './util';
 import { facetedStateTreeF } from './facetedModel';
-// for settings that are config dependent
-function postNoConfigF() {
+// for settings that are not config dependent
+function keyNoConfigPostFix() {
     return typeof window !== 'undefined'
         ? [window.location.host, window.location.pathname].join('-')
         : 'empty';
 }
-// for settings that are not config dependent
-function postF() {
+// for settings that are config dependent
+function keyConfigPostFix() {
     return typeof window !== 'undefined'
         ? [
-            postNoConfigF(),
+            keyNoConfigPostFix(),
             new URLSearchParams(window.location.search).get('config'),
         ].join('-')
         : 'empty';
 }
+function recentlyUsedK(assemblyNames) {
+    return ['recentlyUsedTracks', keyConfigPostFix(), assemblyNames.join(',')]
+        .filter(f => !!f)
+        .join('-');
+}
+// this has a extra } at the end because that's how it was initially
+// released
+function favoritesK() {
+    return `favoriteTracks-${keyConfigPostFix()}}`;
+}
+function collapsedK(assemblyNames, viewType) {
+    return [
+        'collapsedCategories',
+        keyConfigPostFix(),
+        assemblyNames.join(','),
+        viewType,
+    ].join('-');
+}
+function sortTrackNamesK() {
+    return 'sortTrackNames';
+}
+function sortCategoriesK() {
+    return 'sortCategories';
+}
+function localStorageGetJSON(key, defaultValue) {
+    var _a;
+    return JSON.parse((_a = localStorageGetItem(key)) !== null && _a !== void 0 ? _a : defaultValue);
+}
+function localStorageSetJSON(key, val) {
+    localStorageSetItem(key, JSON.stringify(val));
+}
 const MAX_RECENTLY_USED = 10;
 /**
  * #stateModel HierarchicalTrackSelectorWidget
@@ -38,22 +69,6 @@ export default function stateTreeFactory(pluginManager) {
          * #property
          */
         type: types.literal('HierarchicalTrackSelectorWidget'),
-        /**
-         * #property
-         */
-        initialized: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        collapsed: types.map(types.boolean),
-        /**
-         * #property
-         */
-        sortTrackNames: types.maybe(types.boolean),
-        /**
-         * #property
-         */
-        sortCategories: types.maybe(types.boolean),
         /**
          * #property
          */
@@ -64,9 +79,12 @@ export default function stateTreeFactory(pluginManager) {
         faceted: types.optional(facetedStateTreeF(), {}),
     })
         .volatile(() => ({
-        favorites: [],
+        favorites: localStorageGetJSON(favoritesK(), '[]'),
         recentlyUsed: [],
         selection: [],
+        sortTrackNames: !!localStorageGetJSON(sortTrackNamesK(), 'false'),
+        sortCategories: !!localStorageGetJSON(sortCategoriesK(), 'false'),
+        collapsed: observable.map(),
         filterText: '',
         recentlyUsedCounter: 0,
         favoritesCounter: 0,
@@ -97,6 +115,13 @@ export default function stateTreeFactory(pluginManager) {
         get recentlyUsedSet() {
             return new Set(self.recentlyUsed);
         },
+        /**
+         * #getter
+         */
+        get assemblyNames() {
+            var _a;
+            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
+        },
     }))
         .actions(self => ({
         /**
@@ -221,6 +246,12 @@ export default function stateTreeFactory(pluginManager) {
         expandAllCategories() {
             self.collapsed.clear();
         },
+        /**
+         * #action
+         */
+        setCollapsedCategories(str) {
+            self.collapsed.replace(str);
+        },
         /**
          * #action
          */
@@ -261,43 +292,17 @@ export default function stateTreeFactory(pluginManager) {
             const assembly = assemblyManager.get(assemblyName);
             const trackConf = assembly === null || assembly === void 0 ? void 0 : assembly.configuration.sequence;
             const viewType = pluginManager.getViewType(self.view.type);
-            if (!trackConf) {
-                return undefined;
-            }
-            for (const display of trackConf.displays) {
-                if (viewType.displayTypes.some(d => d.name === display.type)) {
-                    return trackConf;
+            if (trackConf) {
+                for (const display of trackConf.displays) {
+                    if (viewType.displayTypes.some(d => d.name === display.type)) {
+                        return trackConf;
+                    }
                 }
             }
             return undefined;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
-        get assemblyNames() {
-            var _a;
-            return ((_a = self.view) === null || _a === void 0 ? void 0 : _a.assemblyNames) || [];
-        },
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get recentlyUsedLocalStorageKey() {
-            return `recentlyUsedTracks-${[postF(), self.assemblyNames.join(',')]
-                .filter(f => !!f)
-                .join('-')}`;
-        },
-        /**
-         * #getter
-         */
-        get favoritesLocalStorageKey() {
-            // this has a extra } at the end because that's how it was initially
-            // released
-            return `favoriteTracks-${postF()}}`;
-        },
         /**
          * #getter
          */
@@ -432,35 +437,6 @@ export default function stateTreeFactory(pluginManager) {
                 self.setCategoryCollapsed(path, true);
             }
         },
-    }))
-        .actions(self => ({
-        afterCreate() {
-            if (!self.initialized) {
-                const session = getSession(self);
-                if (getConf(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'topLevelCategories',
-                ])) {
-                    self.collapseTopLevelCategories();
-                }
-                if (getConf(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'subCategories',
-                ])) {
-                    self.collapseSubCategories();
-                }
-                for (const entry of getConf(session, [
-                    'hierarchical',
-                    'defaultCollapsed',
-                    'categoryNames',
-                ])) {
-                    self.collapsed.set(entry, true);
-                }
-                self.initialized = true;
-            }
-        },
     }))
         .views(self => ({
         /**
@@ -474,13 +450,50 @@ export default function stateTreeFactory(pluginManager) {
         afterAttach() {
             // this should be the first autorun to properly initialize
             addDisposer(self, autorun(() => {
-                self.setRecentlyUsed(JSON.parse(localStorageGetItem(self.recentlyUsedLocalStorageKey) || '[]'));
-                self.setFavorites(JSON.parse(localStorageGetItem(self.favoritesLocalStorageKey) || '[]'));
+                const { assemblyNames, view } = self;
+                self.setRecentlyUsed(localStorageGetJSON(recentlyUsedK(assemblyNames), '[]'));
+                if (view) {
+                    const val = localStorageGetItem(collapsedK(assemblyNames, view.type));
+                    if (!val) {
+                        self.expandAllCategories();
+                        const session = getSession(self);
+                        if (getConf(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'topLevelCategories',
+                        ])) {
+                            self.collapseTopLevelCategories();
+                        }
+                        if (getConf(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'subCategories',
+                        ])) {
+                            self.collapseSubCategories();
+                        }
+                        for (const entry of getConf(session, [
+                            'hierarchical',
+                            'defaultCollapsed',
+                            'categoryNames',
+                        ])) {
+                            self.setCategoryCollapsed(`Tracks-${entry}`, true);
+                        }
+                    }
+                    else {
+                        self.setCollapsedCategories(JSON.parse(val));
+                    }
+                }
             }));
             // this should be the second autorun
             addDisposer(self, autorun(() => {
-                localStorageSetItem(self.favoritesLocalStorageKey, JSON.stringify(self.favorites));
-                localStorageSetItem(self.recentlyUsedLocalStorageKey, JSON.stringify(self.recentlyUsed));
+                const { assemblyNames, collapsed, view } = self;
+                localStorageSetJSON(recentlyUsedK(assemblyNames), self.recentlyUsed);
+                localStorageSetJSON(favoritesK(), self.favorites);
+                localStorageSetJSON(sortTrackNamesK(), self.sortTrackNames);
+                localStorageSetJSON(sortCategoriesK(), self.sortCategories);
+                if (view) {
+                    localStorageSetJSON(collapsedK(assemblyNames, view.type), collapsed);
+                }
             }));
         },
     }));

package/esm/HierarchicalTrackSelectorWidget/util.d.ts

@@ -7,6 +7,6 @@ interface Node {
     children: Node[];
     id: string;
 }
-export declare function findSubCategories(obj: Node[], paths: string[]): boolean;
+export declare function findSubCategories(obj: Node[], paths: string[], depth?: number): boolean;
 export declare function findTopLevelCategories(obj: Node[], paths: string[]): void;
 export {};

package/esm/HierarchicalTrackSelectorWidget/util.js

@@ -21,12 +21,13 @@ export function matches(query, conf, session) {
     return (getTrackName(conf, session).toLowerCase().includes(queryLower) ||
         !!categories.filter(c => c.toLowerCase().includes(queryLower)).length);
 }
-export function findSubCategories(obj, paths) {
+export function findSubCategories(obj, paths, depth = 0) {
     let hasSubs = false;
     for (const elt of obj) {
         if (elt.children.length) {
-            const hasSubCategories = findSubCategories(elt.children, paths);
-            if (hasSubCategories) {
+            const hasSubCategories = findSubCategories(elt.children, paths, depth + 1);
+            // avoid pushing the root "Tracks" node by checking depth>0
+            if (hasSubCategories && depth > 0) {
                 paths.push(elt.id);
             }
         }

package/esm/PluginStoreWidget/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 PluginStoreWidgetF(pluginManager: PluginManager): void;

package/esm/PluginStoreWidget/index.js

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

package/esm/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/esm/index.js

@@ -6,7 +6,7 @@ import AddConnectionWidgetF from './AddConnectionWidget';
 import PluginStoreWidgetF from './PluginStoreWidget';
 import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget';
 const AssemblyManager = lazy(() => import('./AssemblyManager'));
-export default class extends Plugin {
+export default class DataManagementPlugin extends Plugin {
     constructor() {
         super(...arguments);
         this.name = 'DataManagementPlugin';

package/esm/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/esm/ucsc-trackhub/index.js

@@ -1,7 +1,7 @@
 import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 import stateModelFactory from './model';
 import configSchema from './configSchema';
-export default (pluginManager) => {
+export default function UCSCTrackHubConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType({
         name: 'UCSCTrackHubConnection',
         configSchema,
@@ -10,4 +10,4 @@ export default (pluginManager) => {
         description: 'A track or assembly hub in the Track Hub format',
         url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
     }));
-};
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "2.11.0",
+  "version": "2.11.2",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -60,5 +60,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "3d43a820b9274a6160aa4dc15616147f390d9094"
+  "gitHead": "511048cb6965f0bf624c96de244e7fd47fce17d6"
 }