@jbrowse/plugin-data-management 3.7.0 → 4.0.1

package/dist/HierarchicalTrackSelectorWidget/generateHierarchy.js

@@ -1,90 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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");
-const util_2 = require("./util");
-function sortConfs(confs, sortNames, sortCategories) {
-    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) {
-        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, extra, noCategories, menuItems, }) {
-    const hierarchy = { children: [] };
-    const { collapsed, 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));
-    for (const conf of sortConfs(confs, activeSortTrackNames, activeSortCategories)) {
-        const categories = [...((0, configuration_1.readConfObject)(conf, 'category') || [])];
-        if (conf.trackId.endsWith('sessionTrack')) {
-            categories.unshift(' Session tracks');
-        }
-        let currLevel = hierarchy;
-        if (!noCategories) {
-            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),
-                        menuItems,
-                        type: 'category',
-                    };
-                    currLevel.children.push(n);
-                    currLevel = n;
-                }
-                else {
-                    currLevel = ret;
-                }
-            }
-        }
-        const r = currLevel.children.findIndex(elt => elt.children.length);
-        const idx = r === -1 ? currLevel.children.length : r;
-        currLevel.children.splice(idx, 0, {
-            id: [extra, conf.trackId].filter(f => !!f).join(','),
-            trackId: conf.trackId,
-            name: (0, tracks_1.getTrackName)(conf, session),
-            conf,
-            checked: viewTracks.some(f => f.configuration === conf),
-            children: [],
-            type: 'track',
-        });
-    }
-    return hierarchy.children;
-}

package/dist/HierarchicalTrackSelectorWidget/index.d.ts

@@ -1,4 +0,0 @@
-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

@@ -1,59 +0,0 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-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 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({
-            name: 'HierarchicalTrackSelectorWidget',
-            heading: 'Available tracks',
-            configSchema: configSchema_1.default,
-            stateModel: (0, model_1.default)(pluginManager),
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/HierarchicalTrackSelector')))),
-        });
-    });
-}
-var model_2 = require("./model");
-Object.defineProperty(exports, "stateModelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
-var configSchema_2 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });

package/dist/HierarchicalTrackSelectorWidget/model.d.ts

@@ -1,244 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { GridRowId } from '@mui/x-data-grid';
-import type { Instance } from 'mobx-state-tree';
-type MaybeAnyConfigurationModel = AnyConfigurationModel | undefined;
-type MaybeBoolean = boolean | undefined;
-export default function stateTreeFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"HierarchicalTrackSelectorWidget">;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-    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]>;
-        showFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        showOptions: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<boolean>, [undefined]>;
-        panelWidth: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
-    }, {
-        visible: Record<string, boolean>;
-        useShoppingCart: boolean;
-        filters: import("mobx").ObservableMap<string, string[]>;
-    } & {
-        setFilter(key: string, value: string[]): void;
-        setPanelWidth(width: number): number;
-        setUseShoppingCart(f: boolean): void;
-        setFilterText(str: string): void;
-        setShowSparse(f: boolean): void;
-        setShowOptions(f: boolean): void;
-        setShowFilters(f: boolean): void;
-    } & {
-        readonly allTrackConfigurations: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & 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>)[];
-    } & {
-        readonly rows: {
-            readonly id: string;
-            readonly conf: {
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                        [x: string]: any;
-                    } & 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>;
-            readonly name: string;
-            readonly category: string;
-            readonly adapter: string;
-            readonly description: string;
-            readonly metadata: Record<string, unknown>;
-        }[];
-    } & {
-        readonly filteredNonMetadataKeys: string[] | readonly ["category", "adapter", "description"];
-        readonly metadataKeys: string[];
-        readonly filteredMetadataKeys: string[];
-        readonly fields: string[];
-        readonly filteredRows: {
-            readonly id: string;
-            readonly conf: {
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                    setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                        [x: string]: any;
-                    } & 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>;
-            readonly name: string;
-            readonly category: string;
-            readonly adapter: string;
-            readonly description: string;
-            readonly metadata: Record<string, unknown>;
-        }[];
-    } & {
-        setVisible(args: Record<string, boolean>): void;
-        afterAttach(): void;
-    }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
-}, {
-    favorites: string[];
-    recentlyUsed: GridRowId[];
-    selection: AnyConfigurationModel[];
-    sortTrackNames: MaybeBoolean;
-    sortCategories: MaybeBoolean;
-    collapsed: import("mobx").ObservableMap<string, boolean>;
-    filterText: string;
-    recentlyUsedCounter: number;
-    favoritesCounter: number;
-} & {
-    readonly shownTrackIds: Set<string>;
-    readonly selectionSet: Set<{
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>>;
-    readonly favoritesSet: Set<string>;
-    readonly recentlyUsedSet: Set<GridRowId>;
-    readonly assemblyNames: string[];
-} & {
-    setSortTrackNames(val: boolean): void;
-    setSortCategories(val: boolean): void;
-    setSelection(elt: AnyConfigurationModel[]): void;
-    addToSelection(elt: AnyConfigurationModel[]): void;
-    removeFromSelection(elt: AnyConfigurationModel[]): void;
-    clearSelection(): void;
-    addToFavorites(trackId: string): void;
-    removeFromFavorites(trackId: string): void;
-    clearFavorites(): void;
-    setRecentlyUsedCounter(val: number): void;
-    setRecentlyUsed(str: string[]): void;
-    setFavorites(str: string[]): void;
-    setFavoritesCounter(val: number): void;
-    addToRecentlyUsed(id: GridRowId): void;
-    clearRecentlyUsed(): void;
-    setView(view: unknown): void;
-    toggleCategory(pathName: string): void;
-    setCategoryCollapsed(pathName: string, status: boolean): void;
-    expandAllCategories(): void;
-    setCollapsedCategories(str: [string, boolean][]): void;
-    clearFilterText(): void;
-    setFilterText(newText: string): void;
-} & {
-    isSelected(track: AnyConfigurationModel): boolean;
-    isFavorite(trackId: string): boolean;
-    isRecentlyUsed(trackId: string): boolean;
-    getRefSeqTrackConf(assemblyName: string): MaybeAnyConfigurationModel;
-} & {
-    readonly activeSortTrackNames: any;
-    readonly activeSortCategories: any;
-    readonly configAndSessionTrackConfigurations: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>)[];
-    readonly allTrackConfigurations: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>)[];
-    readonly allTrackConfigurationTrackIdSet: Map<any, {
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>>;
-} & {
-    readonly favoriteTracks: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>)[];
-    readonly recentlyUsedTracks: ({
-        [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & 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>)[];
-} & {
-    readonly allTracks: {
-        group: any;
-        tracks: ({
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & 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>)[];
-        noCategories: boolean;
-        menuItems: never[];
-    }[];
-} & {
-    readonly hierarchy: {
-        name: string;
-        id: string;
-        isOpenByDefault: boolean;
-        type: "category";
-        children: {
-            name: any;
-            id: any;
-            type: "category";
-            isOpenByDefault: boolean;
-            menuItems: never[];
-            children: import("./generateHierarchy").TreeNode[];
-        }[];
-    };
-} & {
-    collapseSubCategories(): void;
-    collapseTopLevelCategories(): void;
-} & {
-    readonly hasAnySubcategories: boolean;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type HierarchicalTrackSelectorStateModel = ReturnType<typeof stateTreeFactory>;
-export type HierarchicalTrackSelectorModel = Instance<HierarchicalTrackSelectorStateModel>;
-export {};