@jbrowse/core 3.7.0 → 4.0.0

package/util/tracks.js

@@ -1,168 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.UNSUPPORTED = exports.UNKNOWN = void 0;
-exports.getTrackAssemblyNames = getTrackAssemblyNames;
-exports.getConfAssemblyNames = getConfAssemblyNames;
-exports.getRpcSessionId = getRpcSessionId;
-exports.getParentRenderProps = getParentRenderProps;
-exports.getBlob = getBlob;
-exports.getBlobMap = getBlobMap;
-exports.setBlobMap = setBlobMap;
-exports.storeBlobLocation = storeBlobLocation;
-exports.makeIndex = makeIndex;
-exports.makeIndexType = makeIndexType;
-exports.getFileName = getFileName;
-exports.guessAdapter = guessAdapter;
-exports.guessTrackType = guessTrackType;
-exports.generateUnsupportedTrackConf = generateUnsupportedTrackConf;
-exports.generateUnknownTrackConf = generateUnknownTrackConf;
-exports.getTrackName = getTrackName;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const index_1 = require("./index");
-const configuration_1 = require("../configuration");
-function getTrackAssemblyNames(track) {
-    return getConfAssemblyNames(track.configuration);
-}
-function getConfAssemblyNames(conf) {
-    const trackAssemblyNames = (0, configuration_1.readConfObject)(conf, 'assemblyNames');
-    if (!trackAssemblyNames) {
-        const parent = (0, mobx_state_tree_1.getParent)(conf);
-        if ('sequence' in parent) {
-            return [(0, configuration_1.readConfObject)(parent, 'name')];
-        }
-        else {
-            throw new Error('unknown assembly names');
-        }
-    }
-    return trackAssemblyNames;
-}
-function getRpcSessionId(thisNode) {
-    let highestRpcSessionId;
-    for (let node = thisNode; !(0, mobx_state_tree_1.isRoot)(node); node = (0, mobx_state_tree_1.getParent)(node)) {
-        if ('rpcSessionId' in node) {
-            highestRpcSessionId = node.rpcSessionId;
-        }
-    }
-    if (!highestRpcSessionId) {
-        throw new Error('getRpcSessionId failed, no parent node in the state tree has an `rpcSessionId` attribute');
-    }
-    return highestRpcSessionId;
-}
-function getParentRenderProps(node) {
-    for (let currentNode = (0, mobx_state_tree_1.getParent)(node); !(0, mobx_state_tree_1.isRoot)(currentNode); currentNode = (0, mobx_state_tree_1.getParent)(currentNode)) {
-        if ('renderProps' in currentNode) {
-            return currentNode.renderProps();
-        }
-    }
-    return {};
-}
-exports.UNKNOWN = 'UNKNOWN';
-exports.UNSUPPORTED = 'UNSUPPORTED';
-let blobMap = {};
-function getBlob(id) {
-    return blobMap[id];
-}
-function getBlobMap() {
-    return blobMap;
-}
-function setBlobMap(map) {
-    blobMap = map;
-}
-let counter = 0;
-function storeBlobLocation(location) {
-    if ('blob' in location) {
-        const blobId = `b${Date.now()}-${counter++}`;
-        blobMap[blobId] = location.blob;
-        return { name: location.blob.name, blobId, locationType: 'BlobLocation' };
-    }
-    return location;
-}
-function makeIndex(location, suffix) {
-    if ('uri' in location) {
-        return {
-            uri: location.uri + suffix,
-            locationType: 'UriLocation',
-        };
-    }
-    else if ('localPath' in location) {
-        return {
-            localPath: location.localPath + suffix,
-            locationType: 'LocalPathLocation',
-        };
-    }
-    else {
-        return location;
-    }
-}
-function makeIndexType(name, typeA, typeB) {
-    return (name === null || name === void 0 ? void 0 : name.toUpperCase().endsWith(typeA)) ? typeA : typeB;
-}
-function getFileName(track) {
-    const uri = 'uri' in track ? track.uri : undefined;
-    const localPath = 'localPath' in track ? track.localPath : undefined;
-    const blob = 'blobId' in track ? track : undefined;
-    return ((blob === null || blob === void 0 ? void 0 : blob.name) ||
-        (uri === null || uri === void 0 ? void 0 : uri.slice(uri.lastIndexOf('/') + 1)) ||
-        (localPath === null || localPath === void 0 ? void 0 : localPath.slice(localPath.replace(/\\/g, '/').lastIndexOf('/') + 1)) ||
-        '');
-}
-function guessAdapter(file, index, adapterHint, model) {
-    if (model) {
-        const { pluginManager } = (0, index_1.getEnv)(model);
-        const adapterGuesser = pluginManager.evaluateExtensionPoint('Core-guessAdapterForLocation', (_file, _index, _adapterHint) => {
-            return undefined;
-        });
-        const adapter = adapterGuesser(file, index, adapterHint);
-        if (adapter) {
-            return adapter;
-        }
-    }
-    return {
-        type: exports.UNKNOWN,
-    };
-}
-function guessTrackType(adapterType, model) {
-    if (model) {
-        const session = (0, index_1.getSession)(model);
-        const trackTypeGuesser = (0, index_1.getEnv)(session).pluginManager.evaluateExtensionPoint('Core-guessTrackTypeForLocation', (_adapterName) => {
-            return undefined;
-        });
-        const trackType = trackTypeGuesser(adapterType);
-        if (trackType) {
-            return trackType;
-        }
-    }
-    return 'FeatureTrack';
-}
-function generateUnsupportedTrackConf(trackName, trackUrl, categories) {
-    const conf = {
-        type: 'FeatureTrack',
-        name: `${trackName} (Unsupported)`,
-        description: `Support not yet implemented for "${trackUrl}"`,
-        category: categories,
-        trackId: '',
-    };
-    conf.trackId = (0, index_1.objectHash)(conf);
-    return conf;
-}
-function generateUnknownTrackConf(trackName, trackUrl, categories) {
-    const conf = {
-        type: 'FeatureTrack',
-        name: `${trackName} (Unknown)`,
-        description: `Could not determine track type for "${trackUrl}"`,
-        category: categories,
-        trackId: '',
-    };
-    conf.trackId = (0, index_1.objectHash)(conf);
-    return conf;
-}
-function getTrackName(conf, session) {
-    const trackName = (0, configuration_1.readConfObject)(conf, 'name');
-    if (!trackName && (0, configuration_1.readConfObject)(conf, 'type') === 'ReferenceSequenceTrack') {
-        const asm = session.assemblies.find(a => a.sequence === conf);
-        return asm
-            ? `Reference sequence (${(0, configuration_1.readConfObject)(asm, 'displayName') || (0, configuration_1.readConfObject)(asm, 'name')})`
-            : 'Reference sequence';
-    }
-    return trackName;
-}

package/util/types/index.d.ts

@@ -1,254 +0,0 @@
-import type React from 'react';
-import type { BlobLocation as MUBlobLocation, LocalPathLocation as MULocalPathLocation, NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, UriLocation as MUUriLocation } from './mst';
-import type TextSearchManager from '../../TextSearch/TextSearchManager';
-import type assemblyManager from '../../assemblyManager';
-import type { AnyConfigurationModel } from '../../configuration';
-import type { BaseInternetAccountModel } from '../../pluggableElementTypes/models';
-import type RpcManager from '../../rpc/RpcManager';
-import type { MenuItem } from '../../ui';
-import type { Feature } from '../simpleFeature';
-import type { ThemeOptions } from '@mui/material';
-import type { IAnyStateTreeNode, IStateTreeNode, IType, Instance, SnapshotIn } from 'mobx-state-tree';
-export * from './util';
-export interface AbstractViewContainer extends IStateTreeNode<IType<any, any, any>> {
-    views: AbstractViewModel[];
-    removeView(view: AbstractViewModel): void;
-    addView(typeName: string, initialState?: Record<string, unknown>): AbstractViewModel;
-}
-export declare function isViewContainer(thing: unknown): thing is AbstractViewContainer;
-export type NotificationLevel = 'error' | 'info' | 'warning' | 'success';
-export interface SnackAction {
-    name: React.ReactElement | string;
-    onClick: () => void;
-}
-export type AssemblyManager = Instance<ReturnType<typeof assemblyManager>>;
-export interface BasePlugin {
-    version?: string;
-    name: string;
-    url?: string;
-}
-export interface JBrowsePlugin {
-    name: string;
-    authors: string[];
-    description: string;
-    location: string;
-    url?: string;
-    umdUrl?: string;
-    esmUrl?: string;
-    cjsUrl?: string;
-    license: string;
-    image?: string;
-}
-export type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
-export interface AbstractSessionModel extends AbstractViewContainer {
-    jbrowse: IAnyStateTreeNode;
-    drawerPosition?: string;
-    configuration: AnyConfigurationModel;
-    rpcManager: RpcManager;
-    assemblyNames: string[];
-    assemblies: AnyConfigurationModel[];
-    selection?: unknown;
-    focusedViewId?: string;
-    themeName?: string;
-    hovered: unknown;
-    setHovered: (arg: unknown) => void;
-    setFocusedViewId?: (id: string) => void;
-    allThemes?: () => Record<string, ThemeOptions>;
-    setSelection: (feature: Feature) => void;
-    setSession?: (arg: {
-        name: string;
-        [key: string]: unknown;
-    }) => void;
-    clearSelection: () => void;
-    duplicateCurrentSession?: () => void;
-    notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void;
-    notifyError: (message: string, error?: unknown, extra?: unknown) => void;
-    assemblyManager: AssemblyManager;
-    version: string;
-    getTrackActionMenuItems?: Function;
-    addAssembly?: Function;
-    removeAssembly?: Function;
-    textSearchManager?: TextSearchManager;
-    connections: AnyConfigurationModel[];
-    deleteConnection?: Function;
-    temporaryAssemblies?: unknown[];
-    addTemporaryAssembly?: (arg: Record<string, unknown>) => void;
-    removeTemporaryAssembly?: (arg: string) => void;
-    sessionConnections?: AnyConfigurationModel[];
-    sessionTracks?: AnyConfigurationModel[];
-    connectionInstances?: {
-        name: string;
-        tracks: AnyConfigurationModel[];
-        configuration: AnyConfigurationModel;
-    }[];
-    makeConnection?: Function;
-    breakConnection?: Function;
-    prepareToBreakConnection?: (arg: AnyConfigurationModel) => any;
-    adminMode?: boolean;
-    showWidget?: Function;
-    addWidget?: Function;
-    DialogComponent?: DialogComponentType;
-    DialogProps: any;
-    queueDialog<T extends DialogComponentType>(callback: (doneCallback: () => void) => [T, React.ComponentProps<T>]): void;
-    name: string;
-    id?: string;
-    tracks: AnyConfigurationModel[];
-}
-export declare function isSessionModel(thing: unknown): thing is AbstractSessionModel;
-export interface SessionWithConfigEditing extends AbstractSessionModel {
-    editConfiguration(configuration: AnyConfigurationModel): void;
-}
-export declare function isSessionModelWithConfigEditing(t: unknown): t is SessionWithConfigEditing;
-export interface SessionWithAddTracks extends AbstractSessionModel {
-    addTrackConf(configuration: AnyConfigurationModel | SnapshotIn<AnyConfigurationModel>): void;
-}
-export declare function isSessionWithAddTracks(t: unknown): t is SessionWithAddTracks;
-export interface SessionWithShareURL extends AbstractSessionModel {
-    shareURL: string;
-}
-export declare function isSessionWithShareURL(thing: unknown): thing is SessionWithShareURL;
-export interface Widget {
-    type: string;
-    id: string;
-}
-export interface SessionWithWidgets extends AbstractSessionModel {
-    minimized: boolean;
-    visibleWidget?: Widget;
-    widgets: Map<string | number, Widget>;
-    activeWidgets: Map<string | number, Widget>;
-    hideAllWidgets: () => void;
-    addWidget(typeName: string, id: string, initialState?: Record<string, unknown>, configuration?: {
-        type: string;
-    }): Widget;
-    showWidget(widget: unknown): void;
-    hideWidget(widget: unknown): void;
-}
-export interface SessionWithDrawerWidgets extends SessionWithWidgets {
-    drawerWidth: number;
-    resizeDrawer(arg: number): number;
-    minimizeWidgetDrawer(): void;
-    showWidgetDrawer: () => void;
-    drawerPosition: string;
-    setDrawerPosition(arg: string): void;
-}
-export declare function isSessionModelWithWidgets(thing: unknown): thing is SessionWithWidgets;
-export interface SessionWithConnections {
-    makeConnection: (arg: AnyConfigurationModel) => void;
-}
-export declare function isSessionModelWithConnections(thing: unknown): thing is SessionWithConnections;
-export interface SessionWithConnectionEditing {
-    addConnectionConf: (arg: AnyConfigurationModel) => void;
-}
-export declare function isSessionModelWithConnectionEditing(thing: unknown): thing is SessionWithConnectionEditing;
-export interface SessionWithSessionPlugins extends AbstractSessionModel {
-    sessionPlugins: JBrowsePlugin[];
-    addSessionPlugin: Function;
-    removeSessionPlugin: Function;
-}
-export declare function isSessionWithSessionPlugins(thing: unknown): thing is SessionWithSessionPlugins;
-export interface SelectionContainer extends AbstractSessionModel {
-    selection?: unknown;
-    setSelection(thing: unknown): void;
-}
-export declare function isSelectionContainer(thing: unknown): thing is SelectionContainer;
-export interface SessionWithFocusedViewAndDrawerWidgets extends SessionWithDrawerWidgets {
-    focusedViewId: string | undefined;
-    setFocusedViewId(id: string): void;
-}
-export interface AbstractViewModel {
-    id: string;
-    type: string;
-    width: number;
-    minimized: boolean;
-    setWidth(width: number): void;
-    setMinimized(flag: boolean): void;
-    displayName: string | undefined;
-    setDisplayName: (arg: string) => void;
-    menuItems: () => MenuItem[];
-}
-export declare function isViewModel(thing: unknown): thing is AbstractViewModel;
-export interface AbstractTrackModel {
-    id: string;
-    displays: AbstractDisplayModel[];
-    configuration: AnyConfigurationModel;
-}
-export declare function isTrackModel(thing: unknown): thing is AbstractTrackModel;
-export interface AbstractDisplayModel {
-    id: string;
-    parentTrack: AbstractTrackModel;
-    renderDelay: number;
-    rendererType: any;
-    cannotBeRenderedReason?: string;
-}
-export declare function isDisplayModel(thing: unknown): thing is AbstractDisplayModel;
-export interface TrackViewModel extends AbstractViewModel {
-    showTrack(trackId: string): void;
-    hideTrack(trackId: string): void;
-}
-export declare function isTrackViewModel(thing: unknown): thing is TrackViewModel;
-export interface AbstractRootModel {
-    jbrowse: IAnyStateTreeNode;
-    session?: AbstractSessionModel;
-    setDefaultSession?(): void;
-    adminMode?: boolean;
-    error?: unknown;
-}
-export interface AppRootModel extends AbstractRootModel {
-    internetAccounts: BaseInternetAccountModel[];
-    findAppropriateInternetAccount(location: UriLocation): BaseInternetAccountModel | undefined;
-}
-export declare function isAppRootModel(thing: unknown): thing is AppRootModel;
-export interface RootModelWithInternetAccounts extends AbstractRootModel {
-    internetAccounts: BaseInternetAccountModel[];
-    findAppropriateInternetAccount(location: UriLocation): BaseInternetAccountModel | undefined;
-}
-export declare function isRootModelWithInternetAccounts(thing: unknown): thing is RootModelWithInternetAccounts;
-export interface AbstractMenuManager {
-    appendMenu(menuName: string): void;
-    insertMenu(menuName: string, position: number): number;
-    insertInMenu(menuName: string, menuItem: MenuItem, position: number): number;
-    appendToMenu(menuName: string, menuItem: MenuItem): number;
-    appendToSubMenu(menuPath: string[], menuItem: MenuItem): number;
-    insertInSubMenu(menuPath: string[], menuItem: MenuItem, position: number): number;
-}
-export declare function isAbstractMenuManager(thing: unknown): thing is AbstractMenuManager;
-export interface NoAssemblyRegion extends SnapshotIn<typeof MUNoAssemblyRegion> {
-}
-export interface Region extends SnapshotIn<typeof MUIRegion> {
-}
-export interface AugmentedRegion extends Region {
-    originalRefName?: string;
-}
-export interface LocalPathLocation extends SnapshotIn<typeof MULocalPathLocation> {
-}
-export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
-}
-export declare function isUriLocation(location: unknown): location is UriLocation;
-export declare function isLocalPathLocation(location: unknown): location is LocalPathLocation;
-export declare function isBlobLocation(location: unknown): location is BlobLocation;
-export declare class AuthNeededError extends Error {
-    message: string;
-    url: string;
-    constructor(message: string, url: string);
-}
-export declare class RetryError extends Error {
-    message: string;
-    internetAccountId: string;
-    constructor(message: string, internetAccountId: string);
-}
-export declare function isAuthNeededException(exception: unknown): exception is AuthNeededError;
-export declare function isRetryException(exception: Error): boolean;
-export interface BlobLocation extends SnapshotIn<typeof MUBlobLocation> {
-}
-export type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
-export interface PreUriLocation {
-    uri: string;
-}
-export interface PreLocalPathLocation {
-    localPath: string;
-}
-export interface PreBlobLocation {
-    blob: File;
-}
-export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
-export { default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -1,172 +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 __exportStar = (this && this.__exportStar) || function(m, exports) {
-    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.TextSearchManager = exports.RetryError = exports.AuthNeededError = void 0;
-exports.isViewContainer = isViewContainer;
-exports.isSessionModel = isSessionModel;
-exports.isSessionModelWithConfigEditing = isSessionModelWithConfigEditing;
-exports.isSessionWithAddTracks = isSessionWithAddTracks;
-exports.isSessionWithShareURL = isSessionWithShareURL;
-exports.isSessionModelWithWidgets = isSessionModelWithWidgets;
-exports.isSessionModelWithConnections = isSessionModelWithConnections;
-exports.isSessionModelWithConnectionEditing = isSessionModelWithConnectionEditing;
-exports.isSessionWithSessionPlugins = isSessionWithSessionPlugins;
-exports.isSelectionContainer = isSelectionContainer;
-exports.isViewModel = isViewModel;
-exports.isTrackModel = isTrackModel;
-exports.isDisplayModel = isDisplayModel;
-exports.isTrackViewModel = isTrackViewModel;
-exports.isAppRootModel = isAppRootModel;
-exports.isRootModelWithInternetAccounts = isRootModelWithInternetAccounts;
-exports.isAbstractMenuManager = isAbstractMenuManager;
-exports.isUriLocation = isUriLocation;
-exports.isLocalPathLocation = isLocalPathLocation;
-exports.isBlobLocation = isBlobLocation;
-exports.isAuthNeededException = isAuthNeededException;
-exports.isRetryException = isRetryException;
-const mobx_state_tree_1 = require("mobx-state-tree");
-__exportStar(require("./util"), exports);
-function isViewContainer(thing) {
-    return ((0, mobx_state_tree_1.isStateTreeNode)(thing) &&
-        'removeView' in thing &&
-        'addView' in thing &&
-        'views' in thing);
-}
-function isSessionModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'rpcManager' in thing &&
-        'configuration' in thing);
-}
-function isSessionModelWithConfigEditing(t) {
-    return isSessionModel(t) && 'editConfiguration' in t;
-}
-function isSessionWithAddTracks(t) {
-    return (isSessionModel(t) && 'addTrackConf' in t && !t.disableAddTracks);
-}
-function isSessionWithShareURL(thing) {
-    return isSessionModel(thing) && 'shareURL' in thing && !!thing.shareURL;
-}
-function isSessionModelWithWidgets(thing) {
-    return isSessionModel(thing) && 'widgets' in thing;
-}
-function isSessionModelWithConnections(thing) {
-    return isSessionModel(thing) && 'makeConnection' in thing;
-}
-function isSessionModelWithConnectionEditing(thing) {
-    return isSessionModel(thing) && 'addConnectionConf' in thing;
-}
-function isSessionWithSessionPlugins(thing) {
-    return isSessionModel(thing) && 'sessionPlugins' in thing;
-}
-function isSelectionContainer(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'selection' in thing &&
-        'setSelection' in thing);
-}
-function isViewModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'width' in thing &&
-        'setWidth' in thing);
-}
-function isTrackModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'configuration' in thing &&
-        thing.configuration.trackId);
-}
-function isDisplayModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'configuration' in thing &&
-        thing.configuration.displayId);
-}
-function isTrackViewModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'showTrack' in thing &&
-        'hideTrack' in thing);
-}
-function isAppRootModel(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'findAppropriateInternetAccount' in thing);
-}
-function isRootModelWithInternetAccounts(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'internetAccounts' in thing &&
-        'findAppropriateInternetAccount' in thing);
-}
-function isAbstractMenuManager(thing) {
-    return (typeof thing === 'object' &&
-        thing !== null &&
-        'appendMenu' in thing &&
-        'appendToSubMenu' in thing);
-}
-function isUriLocation(location) {
-    return (typeof location === 'object' &&
-        location !== null &&
-        'uri' in location &&
-        !!location.uri);
-}
-function isLocalPathLocation(location) {
-    return (typeof location === 'object' &&
-        location !== null &&
-        'localPath' in location &&
-        !!location.localPath);
-}
-function isBlobLocation(location) {
-    return (typeof location === 'object' &&
-        location !== null &&
-        'blobId' in location &&
-        !!location.blobId);
-}
-class AuthNeededError extends Error {
-    constructor(message, url) {
-        super(message);
-        this.message = message;
-        this.url = url;
-        this.name = 'AuthNeededError';
-        Object.setPrototypeOf(this, AuthNeededError.prototype);
-    }
-}
-exports.AuthNeededError = AuthNeededError;
-class RetryError extends Error {
-    constructor(message, internetAccountId) {
-        super(message);
-        this.message = message;
-        this.internetAccountId = internetAccountId;
-        this.name = 'RetryError';
-    }
-}
-exports.RetryError = RetryError;
-function isAuthNeededException(exception) {
-    return (exception instanceof Error &&
-        (exception.name === 'AuthNeededError' ||
-            exception.url !== undefined));
-}
-function isRetryException(exception) {
-    return (exception.name === 'RetryError' ||
-        exception.internetAccountId !== undefined);
-}
-var TextSearchManager_1 = require("../../TextSearch/TextSearchManager");
-Object.defineProperty(exports, "TextSearchManager", { enumerable: true, get: function () { return __importDefault(TextSearchManager_1).default; } });