@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/dist/HierarchicalTrackSelectorWidget/facetedModel.js

@@ -1,41 +1,23 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.facetedStateTreeF = facetedStateTreeF;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const util_1 = require("./util");
 const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-const util_2 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_2 = require("./components/faceted/util");
 const facetedUtil_1 = require("./facetedUtil");
-const util_3 = require("./components/faceted/util");
+const util_3 = require("./util");
 const nonMetadataKeys = ['category', 'adapter', 'description'];
-/**
- * #stateModel FacetedModel
- */
 function facetedStateTreeF() {
     return mobx_state_tree_1.types
         .model('FacetedModel', {
-        /**
-         * #property
-         */
         filterText: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.string, ''),
-        /**
-         * #property
-         */
-        showSparse: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => JSON.parse((0, util_2.localStorageGetItem)('facet-showSparse') || 'false')),
-        /**
-         * #property
-         */
-        showFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => JSON.parse((0, util_2.localStorageGetItem)('facet-showFilters') || 'true')),
-        /**
-         * #property
-         */
-        showOptions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => JSON.parse((0, util_2.localStorageGetItem)('facet-showTableOptions') || 'false')),
-        /**
-         * #property
-         */
-        panelWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, () => JSON.parse((0, util_2.localStorageGetItem)('facet-panelWidth') || '400')),
+        showSparse: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('facet-showSparse', false)),
+        showFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('facet-showFilters', true)),
+        showOptions: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.boolean, () => (0, util_1.localStorageGetBoolean)('facet-showTableOptions', false)),
+        panelWidth: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, () => (0, util_1.localStorageGetNumber)('facet-panelWidth', 400)),
     })
         .volatile(() => ({
         visible: {},
@@ -43,70 +25,43 @@ function facetedStateTreeF() {
         filters: mobx_1.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 (0, mobx_state_tree_1.getParent)(self).allTrackConfigurations;
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get rows() {
-            const session = (0, util_2.getSession)(self);
+            const session = (0, util_1.getSession)(self);
             const { allTrackConfigurations, filterText } = self;
             return allTrackConfigurations
-                .filter(conf => (0, util_1.matches)(filterText, conf, session))
+                .filter(conf => (0, util_3.matches)(filterText, conf, session))
                 .map(track => {
                 var _a, _b;
-                return {
+                return ({
                     id: track.trackId,
                     conf: track,
                     name: (0, tracks_1.getTrackName)(track, session),
@@ -114,35 +69,24 @@ function facetedStateTreeF() {
                     adapter: (_b = (0, configuration_1.readConfObject)(track, 'adapter')) === null || _b === void 0 ? void 0 : _b.type,
                     description: (0, configuration_1.readConfObject)(track, 'description'),
                     metadata: (0, configuration_1.readConfObject)(track, 'metadata'),
-                };
+                });
             });
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get filteredNonMetadataKeys() {
             return self.showSparse
                 ? nonMetadataKeys
                 : (0, facetedUtil_1.findNonSparseKeys)(nonMetadataKeys, self.rows, (r, f) => r[f]);
         },
-        /**
-         * #getter
-         */
         get metadataKeys() {
             return [...new Set(self.rows.flatMap(row => (0, facetedUtil_1.getRootKeys)(row.metadata)))];
         },
         get filteredMetadataKeys() {
             return self.showSparse
                 ? this.metadataKeys
-                : (0, facetedUtil_1.findNonSparseKeys)(this.metadataKeys, self.rows, 
-                // @ts-expect-error
-                (r, f) => r.metadata[f]);
+                : (0, facetedUtil_1.findNonSparseKeys)(this.metadataKeys, self.rows, (r, f) => r.metadata[f]);
         },
-        /**
-         * #getter
-         */
         get fields() {
             return [
                 'name',
@@ -150,20 +94,14 @@ function facetedStateTreeF() {
                 ...this.filteredMetadataKeys.map(m => `metadata.${m}`),
             ];
         },
-        /**
-         * #getter
-         */
         get filteredRows() {
             const arrFilters = [...self.filters.entries()]
                 .filter(f => f[1].length > 0)
                 .map(([key, val]) => [key, new Set(val)]);
-            return self.rows.filter(row => arrFilters.every(([key, val]) => val.has((0, util_3.getRowStr)(key, row))));
+            return self.rows.filter(row => arrFilters.every(([key, val]) => val.has((0, util_2.getRowStr)(key, row))));
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setVisible(args) {
             self.visible = args;
         },

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

@@ -4,11 +4,8 @@ exports.generateHierarchy = generateHierarchy;
 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 [
@@ -23,8 +20,6 @@ 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]);
@@ -49,18 +44,13 @@ function generateHierarchy({ model, trackConfs, extra, noCategories, menuItems,
     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;
         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);
@@ -84,9 +74,6 @@ function generateHierarchy({ model, trackConfs, extra, noCategories, menuItems,
                 }
             }
         }
-        // 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/dist/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/dist/HierarchicalTrackSelectorWidget/index.js

@@ -15,23 +15,33 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.configSchema = exports.stateModelFactory = void 0;
 exports.default = HierarchicalTrackSelectorWidgetF;
-const model_1 = __importDefault(require("./model"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const react_1 = require("react");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
+const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 function HierarchicalTrackSelectorWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
         return new pluggableElementTypes_1.WidgetType({

package/dist/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;