@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/esm/HierarchicalTrackSelectorWidget/facetedModel.js

@@ -1,38 +1,20 @@
-import { addDisposer, getParent, types } from 'mobx-state-tree';
-import { matches } from './util';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
+import { getSession, localStorageGetBoolean, localStorageGetNumber, } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
-import { getSession, localStorageGetItem } from '@jbrowse/core/util';
 import { autorun, observable } from 'mobx';
-import { getRootKeys, findNonSparseKeys } from './facetedUtil';
+import { addDisposer, getParent, types } from 'mobx-state-tree';
 import { getRowStr } from './components/faceted/util';
+import { findNonSparseKeys, getRootKeys } from './facetedUtil';
+import { matches } from './util';
 const nonMetadataKeys = ['category', 'adapter', 'description'];
-/**
- * #stateModel FacetedModel
- */
 export function facetedStateTreeF() {
     return types
         .model('FacetedModel', {
-        /**
-         * #property
-         */
         filterText: types.optional(types.string, ''),
-        /**
-         * #property
-         */
-        showSparse: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('facet-showSparse') || 'false')),
-        /**
-         * #property
-         */
-        showFilters: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('facet-showFilters') || 'true')),
-        /**
-         * #property
-         */
-        showOptions: types.optional(types.boolean, () => JSON.parse(localStorageGetItem('facet-showTableOptions') || 'false')),
-        /**
-         * #property
-         */
-        panelWidth: types.optional(types.number, () => JSON.parse(localStorageGetItem('facet-panelWidth') || '400')),
+        showSparse: types.optional(types.boolean, () => localStorageGetBoolean('facet-showSparse', false)),
+        showFilters: types.optional(types.boolean, () => localStorageGetBoolean('facet-showFilters', true)),
+        showOptions: types.optional(types.boolean, () => localStorageGetBoolean('facet-showTableOptions', false)),
+        panelWidth: types.optional(types.number, () => localStorageGetNumber('facet-panelWidth', 400)),
     })
         .volatile(() => ({
         visible: {},
@@ -40,62 +22,35 @@ export function facetedStateTreeF() {
         filters: observable.map(),
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setFilter(key, value) {
             self.filters.set(key, value);
         },
-        /**
-         * #action
-         */
         setPanelWidth(width) {
             self.panelWidth = width;
             return self.panelWidth;
         },
-        /**
-         * #action
-         */
         setUseShoppingCart(f) {
             self.useShoppingCart = f;
         },
-        /**
-         * #action
-         */
         setFilterText(str) {
             self.filterText = str;
         },
-        /**
-         * #action
-         */
         setShowSparse(f) {
             self.showSparse = f;
         },
-        /**
-         * #action
-         */
         setShowOptions(f) {
             self.showOptions = f;
         },
-        /**
-         * #action
-         */
         setShowFilters(f) {
             self.showFilters = f;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get allTrackConfigurations() {
             return getParent(self).allTrackConfigurations;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get rows() {
             const session = getSession(self);
             const { allTrackConfigurations, filterText } = self;
@@ -103,7 +58,7 @@ export function facetedStateTreeF() {
                 .filter(conf => matches(filterText, conf, session))
                 .map(track => {
                 var _a, _b;
-                return {
+                return ({
                     id: track.trackId,
                     conf: track,
                     name: getTrackName(track, session),
@@ -111,35 +66,24 @@ export function facetedStateTreeF() {
                     adapter: (_b = readConfObject(track, 'adapter')) === null || _b === void 0 ? void 0 : _b.type,
                     description: readConfObject(track, 'description'),
                     metadata: readConfObject(track, 'metadata'),
-                };
+                });
             });
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get filteredNonMetadataKeys() {
             return self.showSparse
                 ? nonMetadataKeys
                 : findNonSparseKeys(nonMetadataKeys, self.rows, (r, f) => r[f]);
         },
-        /**
-         * #getter
-         */
         get metadataKeys() {
             return [...new Set(self.rows.flatMap(row => getRootKeys(row.metadata)))];
         },
         get filteredMetadataKeys() {
             return self.showSparse
                 ? this.metadataKeys
-                : findNonSparseKeys(this.metadataKeys, self.rows, 
-                // @ts-expect-error
-                (r, f) => r.metadata[f]);
+                : findNonSparseKeys(this.metadataKeys, self.rows, (r, f) => r.metadata[f]);
         },
-        /**
-         * #getter
-         */
         get fields() {
             return [
                 'name',
@@ -147,9 +91,6 @@ export function facetedStateTreeF() {
                 ...this.filteredMetadataKeys.map(m => `metadata.${m}`),
             ];
         },
-        /**
-         * #getter
-         */
         get filteredRows() {
             const arrFilters = [...self.filters.entries()]
                 .filter(f => f[1].length > 0)
@@ -158,9 +99,6 @@ export function facetedStateTreeF() {
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setVisible(args) {
             self.visible = args;
         },

package/esm/HierarchicalTrackSelectorWidget/filterTracks.d.ts

@@ -1,4 +1,4 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function filterTracks(tracks: AnyConfigurationModel[], self: {
     view?: {
         type: string;

package/esm/HierarchicalTrackSelectorWidget/filterTracks.js

@@ -1,4 +1,4 @@
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { getEnv, getSession, notEmpty } from '@jbrowse/core/util';
 import { hasAllOverlap, hasAnyOverlap } from './util';
 export function filterTracks(tracks, self) {

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.d.ts

@@ -1,5 +1,5 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { MenuItem } from '@jbrowse/core/ui';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { MenuItem } from '@jbrowse/core/ui';
 export interface TreeTrackNode {
     name: string;
     id: string;

package/esm/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -1,11 +1,8 @@
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
-// locals
 import { matches } from './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 [
@@ -20,8 +17,6 @@ function sortConfs(confs, sortNames, sortCategories) {
         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]);
@@ -46,18 +41,13 @@ export function generateHierarchy({ model, trackConfs, extra, noCategories, menu
     const session = getSession(model);
     const viewTracks = view.tracks;
     const confs = trackConfs.filter(conf => 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 = [...(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;
         if (!noCategories) {
-            // 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);
@@ -81,9 +71,6 @@ export function generateHierarchy({ model, trackConfs, extra, noCategories, menu
                 }
             }
         }
-        // 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, {

package/esm/HierarchicalTrackSelectorWidget/index.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 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

@@ -1,7 +1,7 @@
-import stateModelFactory from './model';
-import configSchema from './configSchema';
-import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
 import { lazy } from 'react';
+import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+import stateModelFactory from './model';
 export default function HierarchicalTrackSelectorWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new WidgetType({

package/esm/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,27 +1,12 @@
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
 type MaybeBoolean = boolean | undefined;
-/**
- * #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
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    /**
-     * #property
-     */
     faceted: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         filterText: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
         showSparse: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
@@ -101,50 +86,17 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
 }, {
-    /**
-     * #volatile
-     */
     favorites: string[];
-    /**
-     * #volatile
-     */
     recentlyUsed: string[];
-    /**
-     * #volatile
-     */
     selection: AnyConfigurationModel[];
-    /**
-     * #volatile
-     */
     sortTrackNames: MaybeBoolean;
-    /**
-     * #volatile
-     */
     sortCategories: MaybeBoolean;
-    /**
-     * #volatile
-     */
     collapsed: import("mobx").ObservableMap<string, boolean>;
-    /**
-     * #volatile
-     */
     filterText: string;
-    /**
-     * #volatile
-     */
     recentlyUsedCounter: number;
-    /**
-     * #volatile
-     */
     favoritesCounter: number;
 } & {
-    /**
-     * #getter
-     */
     readonly shownTrackIds: Set<string>;
-    /**
-     * #getter
-     */
     readonly selectionSet: Set<{
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -156,137 +108,40 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
-    /**
-     * #getter
-     */
     readonly favoritesSet: Set<string>;
-    /**
-     * #getter
-     */
     readonly recentlyUsedSet: Set<string>;
-    /**
-     * #getter
-     */
     readonly assemblyNames: string[];
 } & {
-    /**
-     * #action
-     */
     setSortTrackNames(val: boolean): void;
-    /**
-     * #action
-     */
     setSortCategories(val: boolean): void;
-    /**
-     * #action
-     */
     setSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     addToSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     removeFromSelection(elt: AnyConfigurationModel[]): void;
-    /**
-     * #action
-     */
     clearSelection(): void;
-    /**
-     * #action
-     */
     addToFavorites(trackId: string): void;
-    /**
-     * #action
-     */
     removeFromFavorites(trackId: string): void;
-    /**
-     * #action
-     */
     clearFavorites(): void;
-    /**
-     * #action
-     */
     setRecentlyUsedCounter(val: number): void;
-    /**
-     * #action
-     */
     setRecentlyUsed(str: string[]): void;
-    /**
-     * #action
-     */
     setFavorites(str: string[]): void;
-    /**
-     * #action
-     */
     setFavoritesCounter(val: number): void;
-    /**
-     * #action
-     */
     addToRecentlyUsed(id: string): void;
-    /**
-     * #action
-     */
     clearRecentlyUsed(): void;
-    /**
-     * #action
-     */
     setView(view: unknown): void;
-    /**
-     * #action
-     */
     toggleCategory(pathName: string): void;
-    /**
-     * #action
-     */
     setCategoryCollapsed(pathName: string, status: boolean): void;
-    /**
-     * #action
-     */
     expandAllCategories(): void;
-    /**
-     * #action
-     */
     setCollapsedCategories(str: [string, boolean][]): void;
-    /**
-     * #action
-     */
     clearFilterText(): void;
-    /**
-     * #action
-     */
     setFilterText(newText: string): void;
 } & {
-    /**
-     * #method
-     */
     isSelected(track: AnyConfigurationModel): boolean;
-    /**
-     * #method
-     */
     isFavorite(trackId: string): boolean;
-    /**
-     * #method
-     */
     isRecentlyUsed(trackId: string): boolean;
-    /**
-     * #method
-     */
     getRefSeqTrackConf(assemblyName: string): MaybeAnyConfigurationModel;
 } & {
-    /**
-     * #getter
-     */
     readonly activeSortTrackNames: any;
-    /**
-     * #getter
-     */
     readonly activeSortCategories: any;
-    /**
-     * #getter
-     * filter out tracks that don't match the current assembly/display types
-     */
     readonly configAndSessionTrackConfigurations: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -298,9 +153,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
-    /**
-     * #getter
-     */
     readonly allTrackConfigurations: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -312,9 +164,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
-    /**
-     * #getter
-     */
     readonly allTrackConfigurationTrackIdSet: Map<any, {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -327,10 +176,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>>;
 } & {
-    /**
-     * #getter
-     * filters out tracks that are not in the favorites group
-     */
     readonly favoriteTracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -342,10 +187,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
-    /**
-     * #getter
-     * filters out tracks that are not in the recently used group
-     */
     readonly recentlyUsedTracks: ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -358,9 +199,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
     } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)[];
 } & {
-    /**
-     * #getter
-     */
     readonly allTracks: {
         group: any;
         tracks: ({
@@ -378,9 +216,6 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         menuItems: never[];
     }[];
 } & {
-    /**
-     * #getter
-     */
     readonly hierarchy: {
         name: string;
         id: string;
@@ -396,18 +231,9 @@ export default function stateTreeFactory(pluginManager: PluginManager): import("
         }[];
     };
 } & {
-    /**
-     * #action
-     */
     collapseSubCategories(): void;
-    /**
-     * #action
-     */
     collapseTopLevelCategories(): void;
 } & {
-    /**
-     * #getter
-     */
     readonly hasAnySubcategories: boolean;
 } & {
     afterAttach(): void;