@jbrowse/core 2.6.3 → 2.7.1

package/util/types/index.d.ts

@@ -8,6 +8,7 @@ import { NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, LocalPathL
 import RpcManager from '../../rpc/RpcManager';
 import { Feature } from '../simpleFeature';
 import { BaseInternetAccountModel } from '../../pluggableElementTypes/models';
+import { ThemeOptions } from '@mui/material';
 export * from './util';
 /** abstract type for a model that contains multiple views */
 export interface AbstractViewContainer extends IStateTreeNode<IType<any, unknown, any>> {
@@ -42,16 +43,25 @@ export interface JBrowsePlugin {
 export type DialogComponentType = React.LazyExoticComponent<React.FC<any>> | React.FC<any>;
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer {
+    jbrowse: IAnyStateTreeNode;
     drawerPosition?: string;
-    setSelection(feature: Feature): void;
-    clearSelection(): void;
     configuration: AnyConfigurationModel;
     rpcManager: RpcManager;
     assemblyNames: string[];
     assemblies: AnyConfigurationModel[];
     selection?: unknown;
-    duplicateCurrentSession?(): void;
-    notify(message: string, level?: NotificationLevel, action?: SnackAction): void;
+    focusedViewId?: string;
+    themeName?: string;
+    setFocusedViewId?: (id: string) => void;
+    allThemes?: () => Record<string, ThemeOptions | undefined>;
+    setSelection: (feature: Feature) => void;
+    setSession?: (arg: {
+        name: string;
+        [key: string]: unknown;
+    }) => void;
+    clearSelection: () => void;
+    duplicateCurrentSession?: () => void;
+    notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void;
     assemblyManager: AssemblyManager;
     version: string;
     getTrackActionMenuItems?: Function;
@@ -60,13 +70,19 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     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;
@@ -88,6 +104,11 @@ export interface SessionWithConfigEditing extends AbstractSessionModel {
     addTrackConf(configuration: AnyConfigurationModel | SnapshotIn<AnyConfigurationModel>): void;
 }
 export declare function isSessionWithAddTracks(thing: unknown): thing is SessionWithConfigEditing;
+/** abstract interface for a session allows adding tracks */
+export interface SessionWithShareURL extends AbstractSessionModel {
+    shareURL: string;
+}
+export declare function isSessionWithShareURL(thing: unknown): thing is SessionWithShareURL;
 export interface Widget {
     type: string;
     id: string;
@@ -134,6 +155,11 @@ export interface SelectionContainer extends AbstractSessionModel {
     setSelection(thing: unknown): void;
 }
 export declare function isSelectionContainer(thing: unknown): thing is SelectionContainer;
+/** abstract interface for a session allows applying focus to views and widgets */
+export interface SessionWithFocusedViewAndDrawerWidgets extends SessionWithDrawerWidgets {
+    focusedViewId: string | undefined;
+    setFocusedViewId(id: string): void;
+}
 /** minimum interface that all view state models must implement */
 export interface AbstractViewModel {
     id: string;
@@ -228,14 +254,14 @@ export declare function isRetryException(exception: Error): boolean;
 export interface BlobLocation extends SnapshotIn<typeof MUBlobLocation> {
 }
 export type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
-export type PreUriLocation = {
+export interface PreUriLocation {
     uri: string;
-};
-export type PreLocalPathLocation = {
+}
+export interface PreLocalPathLocation {
     localPath: string;
-};
-export type PreBlobLocation = {
+}
+export interface PreBlobLocation {
     blob: File;
-};
+}
 export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
 export { type default as TextSearchManager } from '../../TextSearch/TextSearchManager';

package/util/types/index.js

@@ -14,7 +14,7 @@ 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);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isBlobLocation = exports.isLocalPathLocation = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnectionEditing = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
+exports.isRetryException = exports.isAuthNeededException = exports.RetryError = exports.AuthNeededError = exports.isBlobLocation = exports.isLocalPathLocation = exports.isUriLocation = exports.isAbstractMenuManager = exports.isRootModelWithInternetAccounts = exports.isAppRootModel = exports.isTrackViewModel = exports.isDisplayModel = exports.isTrackModel = exports.isViewModel = exports.isSelectionContainer = exports.isSessionWithSessionPlugins = exports.isSessionModelWithConnectionEditing = exports.isSessionModelWithConnections = exports.isSessionModelWithWidgets = exports.isSessionWithShareURL = exports.isSessionWithAddTracks = exports.isSessionModelWithConfigEditing = exports.isSessionModel = exports.isViewContainer = void 0;
 const mobx_state_tree_1 = require("mobx-state-tree");
 __exportStar(require("./util"), exports);
 function isViewContainer(thing) {
@@ -41,6 +41,10 @@ function isSessionWithAddTracks(thing) {
     isSessionModel(thing) && 'addTrackConf' in thing && !thing.disableAddTracks);
 }
 exports.isSessionWithAddTracks = isSessionWithAddTracks;
+function isSessionWithShareURL(thing) {
+    return isSessionModel(thing) && 'shareURL' in thing && !!thing.shareURL;
+}
+exports.isSessionWithShareURL = isSessionWithShareURL;
 function isSessionModelWithWidgets(thing) {
     return isSessionModel(thing) && 'widgets' in thing;
 }

package/util/types/mst.js

@@ -4,11 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FileLocation = exports.UriLocation = exports.UriLocationRaw = exports.BlobLocation = exports.LocalPathLocation = exports.Region = exports.NoAssemblyRegion = exports.PropTypes = exports.ElementId = void 0;
-const shortid_1 = __importDefault(require("shortid"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 const prop_types_1 = __importDefault(require("prop-types"));
 const mobx_react_1 = require("mobx-react");
-exports.ElementId = mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, shortid_1.default.generate);
+const nanoid_1 = require("../nanoid");
+exports.ElementId = mobx_state_tree_1.types.optional(mobx_state_tree_1.types.identifier, () => (0, nanoid_1.nanoid)());
 // PropTypes that are useful when working with instances of these in react components
 exports.PropTypes = {
     Region: prop_types_1.default.shape({

package/BaseFeatureWidget/BaseFeatureDetail/UriLink.d.ts

@@ -1,7 +0,0 @@
-import React from 'react';
-export default function UriLink({ value, }: {
-    value: {
-        uri: string;
-        baseUri?: string;
-    };
-}): React.JSX.Element;

package/BaseFeatureWidget/BaseFeatureDetail/UriLink.js

@@ -1,13 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
-const util_1 = require("../../util");
-const ui_1 = require("../../ui");
-function UriLink({ value, }) {
-    const href = (0, util_1.getUriLink)(value);
-    return react_1.default.createElement(ui_1.SanitizedHTML, { html: `<a href="${href}">${href}</a>` });
-}
-exports.default = UriLink;