@jbrowse/product-core 2.17.0 → 3.0.0

package/dist/Session/Tracks.js

@@ -5,33 +5,18 @@ exports.isSessionWithTracks = isSessionWithTracks;
 const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseSession_1 = require("./BaseSession");
 const ReferenceManagement_1 = require("./ReferenceManagement");
-/**
- * #stateModel TracksManagerSessionMixin
- * composed of
- * - BaseSessionModel
- * - ReferenceManagementSessionMixin
- */
 function TracksManagerSessionMixin(pluginManager) {
     return mobx_state_tree_1.types
         .compose('TracksManagerSessionMixin', (0, BaseSession_1.BaseSessionModel)(pluginManager), (0, ReferenceManagement_1.ReferenceManagementSessionMixin)(pluginManager))
         .views(self => ({
-        /**
-         * #getter
-         */
         get tracks() {
             return self.jbrowse.tracks;
         },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         addTrackConf(trackConf) {
             return self.jbrowse.addTrackConf(trackConf);
         },
-        /**
-         * #action
-         */
         deleteTrackConf(trackConf) {
             const callbacksToDereferenceTrack = [];
             const dereferenceTypeCount = {};
@@ -46,7 +31,6 @@ function TracksManagerSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithTracks */
 function isSessionWithTracks(thing) {
     return (0, BaseSession_1.isBaseSession)(thing) && 'tracks' in thing;
 }

package/dist/rpcWorker.d.ts

@@ -1,5 +1,5 @@
-import { LoadedPlugin } from '@jbrowse/core/PluginLoader';
-import { PluginConstructor } from '@jbrowse/core/Plugin';
+import type { PluginConstructor } from '@jbrowse/core/Plugin';
+import type { LoadedPlugin } from '@jbrowse/core/PluginLoader';
 export declare function initializeWorker(corePlugins: PluginConstructor[], opts: {
     fetchESM?: (url: string) => Promise<LoadedPlugin>;
     fetchCJS?: (url: string) => Promise<LoadedPlugin>;

package/dist/rpcWorker.js

@@ -4,13 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.initializeWorker = initializeWorker;
-const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
-const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
-const remoteAbortSignals_1 = require("@jbrowse/core/rpc/remoteAbortSignals");
 const PluginLoader_1 = __importDefault(require("@jbrowse/core/PluginLoader"));
+const PluginManager_1 = __importDefault(require("@jbrowse/core/PluginManager"));
+const librpc_web_mod_1 = __importDefault(require("librpc-web-mod"));
 const serialize_error_1 = require("serialize-error");
-// waits for a message from the main thread containing our configuration, which
-// must be sent on boot
 function receiveConfiguration() {
     const configurationP = new Promise(resolve => {
         function listener(e) {
@@ -25,7 +22,6 @@ function receiveConfiguration() {
     return configurationP;
 }
 async function getPluginManager(corePlugins, opts) {
-    // Load runtime plugins
     const config = await receiveConfiguration();
     const pluginLoader = new PluginLoader_1.default(config.plugins, opts).installGlobalReExports(self);
     return new PluginManager_1.default([
@@ -41,7 +37,6 @@ function wrapForRpc(func) {
         return func({
             ...args,
             statusCallback: (message) => {
-                // @ts-expect-error
                 self.rpcServer.emit(channel, message);
             },
         }, rpcDriverClassName);
@@ -53,19 +48,10 @@ async function initializeWorker(corePlugins, opts) {
         const rpcConfig = Object.fromEntries(pluginManager
             .getRpcElements()
             .map(e => [e.name, wrapForRpc(e.execute.bind(e))]));
-        // @ts-expect-error
-        self.rpcServer = new librpc_web_mod_1.default.Server({
-            ...rpcConfig,
-            ...(0, remoteAbortSignals_1.remoteAbortRpcHandler)(),
-            ping: async () => {
-                // the ping method is required by the worker driver for checking the
-                // health of the worker
-            },
-        });
+        self.rpcServer = new librpc_web_mod_1.default.Server(rpcConfig);
         postMessage({ message: 'ready' });
     }
     catch (e) {
         postMessage({ message: 'error', error: (0, serialize_error_1.serializeError)(e) });
     }
-    /* do nothing */
 }

package/dist/ui/AboutDialog.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function AboutDialog({ config, handleClose, }: {
     config: AnyConfigurationModel;
     handleClose: () => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/ui/AboutDialog.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.AboutDialog = AboutDialog;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const Dialog_1 = __importDefault(require("@jbrowse/core/ui/Dialog"));
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
@@ -14,6 +14,5 @@ function AboutDialog({ config, handleClose, }) {
     const trackName = (0, tracks_1.getTrackName)(config, session);
     const { pluginManager } = (0, util_1.getEnv)(session);
     const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutDialogContents_1.default, { session, config });
-    return (react_1.default.createElement(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
-        react_1.default.createElement(AboutComponent, { config: config })));
+    return ((0, jsx_runtime_1.jsx)(Dialog_1.default, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl", children: (0, jsx_runtime_1.jsx)(AboutComponent, { config: config }) }));
 }

package/dist/ui/AboutDialogContents.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AboutDialogContents: ({ config, }: {
     config: AnyConfigurationModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AboutDialogContents;

package/dist/ui/AboutDialogContents.js

@@ -1,42 +1,18 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const clone_1 = __importDefault(require("clone"));
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-// locals
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const FileInfoPanel_1 = __importDefault(require("./FileInfoPanel"));
 const RefNameInfoDialog_1 = __importDefault(require("./RefNameInfoDialog"));
 const useStyles = (0, mui_1.makeStyles)()({
@@ -75,26 +51,17 @@ const AboutDialogContents = (0, mobx_react_1.observer)(function ({ config, }) {
         },
     }, { session, config });
     const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
-    return (react_1.default.createElement("div", { className: classes.content },
-        react_1.default.createElement(BaseCard_1.default, { title: "Configuration" },
-            !hideUris ? (react_1.default.createElement("span", { className: classes.button },
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                        setShowRefNames(true);
-                    } }, "Show ref names"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                        const snap = removeAttr((0, clone_1.default)(conf), 'baseUri');
-                        (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
-                        setCopied(true);
-                        setTimeout(() => {
-                            setCopied(false);
-                        }, 1000);
-                    } }, copied ? 'Copied to clipboard!' : 'Copy config'))) : null,
-            react_1.default.createElement(Attributes_1.default, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
-        ExtraPanel ? (react_1.default.createElement(BaseCard_1.default, { title: ExtraPanel.name },
-            react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
-        react_1.default.createElement(FileInfoPanel_1.default, { config: config }),
-        showRefNames ? (react_1.default.createElement(RefNameInfoDialog_1.default, { config: config, onClose: () => {
-                setShowRefNames(false);
-            } })) : null));
+    return ((0, jsx_runtime_1.jsxs)("div", { className: classes.content, children: [(0, jsx_runtime_1.jsxs)(BaseCard_1.default, { title: "Configuration", children: [!hideUris ? ((0, jsx_runtime_1.jsxs)("span", { className: classes.button, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                                    setShowRefNames(true);
+                                }, children: "Show ref names" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                                    const snap = removeAttr(structuredClone(conf), 'baseUri');
+                                    (0, copy_to_clipboard_1.default)(JSON.stringify(snap, null, 2));
+                                    setCopied(true);
+                                    setTimeout(() => {
+                                        setCopied(false);
+                                    }, 1000);
+                                }, children: copied ? 'Copied to clipboard!' : 'Copy config' })] })) : null, (0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: confPostExt.config, omit: ['displays', 'baseUri', 'refNames', 'formatAbout', 'metadata'], hideUris: hideUris })] }), confPostExt.config.metadata ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "Metadata", children: (0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: confPostExt.config.metadata, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris }) })) : null, ExtraPanel ? ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: ExtraPanel.name, children: (0, jsx_runtime_1.jsx)(ExtraPanel.Component, { config: config }) })) : null, (0, jsx_runtime_1.jsx)(FileInfoPanel_1.default, { config: config }), showRefNames ? ((0, jsx_runtime_1.jsx)(RefNameInfoDialog_1.default, { config: config, onClose: () => {
+                    setShowRefNames(false);
+                } })) : null] }));
 });
 exports.default = AboutDialogContents;

package/dist/ui/FileInfoPanel.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export default function FileInfoPanel({ config, }: {
     config: AnyConfigurationModel;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/ui/FileInfoPanel.js

@@ -1,45 +1,22 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = FileInfoPanel;
-const react_1 = __importStar(require("react"));
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const Attributes_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes"));
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
+const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
 function FileInfoPanel({ config, }) {
     const [error, setError] = (0, react_1.useState)();
     const [info, setInfo] = (0, react_1.useState)();
     const session = (0, util_1.getSession)(config);
     const { rpcManager } = session;
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -62,5 +39,5 @@ function FileInfoPanel({ config, }) {
                 .replaceAll('>', '&gt;')}</pre>`,
         }
         : info || {};
-    return (react_1.default.createElement(BaseCard_1.default, { title: "File info" }, error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : info === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading file data" })) : (react_1.default.createElement(Attributes_1.default, { attributes: details }))));
+    return ((0, jsx_runtime_1.jsx)(BaseCard_1.default, { title: "File info", children: error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : info === undefined ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Loading file data" })) : ((0, jsx_runtime_1.jsx)(Attributes_1.default, { attributes: details })) }));
 }

package/dist/ui/RefNameInfoDialog.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const RefNameInfoDialog: ({ config, onClose, }: {
     config: AnyConfigurationModel;
     onClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default RefNameInfoDialog;

package/dist/ui/RefNameInfoDialog.js

@@ -1,40 +1,18 @@
 "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 (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 __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const material_1 = require("@mui/material");
+const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const mobx_react_1 = require("mobx-react");
 const mui_1 = require("tss-react/mui");
-const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const MAX_REF_NAMES = 10000;
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     container: {
@@ -54,7 +32,6 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
     const [copied, setCopied] = (0, react_1.useState)(false);
     const { rpcManager } = (0, util_1.getSession)(config);
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -64,7 +41,6 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
                         assemblyName,
                         (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
                             adapterConfig,
-                            // hack for synteny adapters
                             regions: [
                                 {
                                     assemblyName,
@@ -94,21 +70,18 @@ const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose
     })
         .filter(f => !!f)
         .join('\n');
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl" },
-        react_1.default.createElement(material_1.DialogContent, { className: classes.container }, error ? (react_1.default.createElement(ui_1.ErrorMessage, { error: error })) : refNames === undefined ? (react_1.default.createElement(ui_1.LoadingEllipses, { message: "Loading refNames" })) : (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    (0, copy_to_clipboard_1.default)(names
-                        .flatMap(([assemblyName, refNames]) => [
-                        `--- ${assemblyName} ---`,
-                        ...refNames,
-                    ])
-                        .filter(f => !!f)
-                        .join('\n'));
-                    setCopied(true);
-                    setTimeout(() => {
-                        setCopied(false);
-                    }, 1000);
-                } }, copied ? 'Copied to clipboard!' : 'Copy ref names'),
-            react_1.default.createElement("pre", { className: classes.refNames }, result))))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl", children: (0, jsx_runtime_1.jsx)(material_1.DialogContent, { className: classes.container, children: error ? ((0, jsx_runtime_1.jsx)(ui_1.ErrorMessage, { error: error })) : refNames === undefined ? ((0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, { message: "Loading refNames" })) : ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                            (0, copy_to_clipboard_1.default)(names
+                                .flatMap(([assemblyName, refNames]) => [
+                                `--- ${assemblyName} ---`,
+                                ...refNames,
+                            ])
+                                .filter(f => !!f)
+                                .join('\n'));
+                            setCopied(true);
+                            setTimeout(() => {
+                                setCopied(false);
+                            }, 1000);
+                        }, children: copied ? 'Copied to clipboard!' : 'Copy ref names' }), (0, jsx_runtime_1.jsx)("pre", { className: classes.refNames, children: result })] })) }) }));
 });
 exports.default = RefNameInfoDialog;

package/esm/RootModel/BaseRootModel.d.ts

@@ -1,38 +1,17 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
-import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
+import RpcManager from '@jbrowse/core/rpc/RpcManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { BaseAssemblyConfigSchema } from '@jbrowse/core/assemblyManager';
+import type { IAnyType, Instance, SnapshotIn } from 'mobx-state-tree';
 export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }: {
     pluginManager: PluginManager;
     jbrowseModelType: IAnyType;
     sessionModelType: IAnyType;
     assemblyConfigSchema: BaseAssemblyConfigSchema;
 }): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     * `jbrowse` is a mapping of the config.json into the in-memory state
-     * tree
-     */
     jbrowse: IAnyType;
-    /**
-     * #property
-     * `session` encompasses the currently active state of the app, including
-     * views open, tracks open in those views, etc.
-     */
     session: import("mobx-state-tree").IMaybe<IAnyType>;
-    /**
-     * #property
-     */
     sessionPath: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     assemblyManager: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IModelType<{
         assemblies: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IModelType<{
             configuration: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<IAnyType>>;
@@ -537,7 +516,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -545,7 +524,7 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
         getReverseRefNameMapForAdapter(adapterConf: {
             [x: string]: unknown;
         }, assemblyName: string | undefined, opts: {
-            signal?: AbortSignal;
+            stopToken?: string;
             sessionId: string;
         }): Promise<{
             [x: string]: string;
@@ -563,28 +542,12 @@ export declare function BaseRootModelFactory({ pluginManager, jbrowseModelType,
     textSearchManager: TextSearchManager;
     pluginManager: PluginManager;
 } & {
-    /**
-     * #action
-     */
     setError(error: unknown): void;
-    /**
-     * #action
-     */
     setSession(sessionSnapshot?: SnapshotIn<IAnyType>): void;
-    /**
-     * #action
-     */
     setDefaultSession(): void;
-    /**
-     * #action
-     */
     setSessionPath(path: string): void;
-    /**
-     * #action
-     */
     renameCurrentSession(newName: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type BaseRootModelType = ReturnType<typeof BaseRootModelFactory>;
 export type BaseRootModel = Instance<BaseRootModelType>;
-/** Type guard for checking if something is a JB root model */
 export declare function isRootModel(thing: unknown): thing is BaseRootModelType;

package/esm/RootModel/BaseRootModel.js

@@ -1,34 +1,13 @@
+import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
 import assemblyManagerFactory from '@jbrowse/core/assemblyManager';
 import RpcManager from '@jbrowse/core/rpc/RpcManager';
-import { cast, getSnapshot, isStateTreeNode, types, } from 'mobx-state-tree';
-import TextSearchManager from '@jbrowse/core/TextSearch/TextSearchManager';
-/**
- * #stateModel BaseRootModel
- * #category root
- * factory function for the Base-level root model shared by all products
- */
+import { cast, getSnapshot, isStateTreeNode, types } from 'mobx-state-tree';
 export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionModelType, assemblyConfigSchema, }) {
     return types
         .model('BaseRootModel', {
-        /**
-         * #property
-         * `jbrowse` is a mapping of the config.json into the in-memory state
-         * tree
-         */
         jbrowse: jbrowseModelType,
-        /**
-         * #property
-         * `session` encompasses the currently active state of the app, including
-         * views open, tracks open in those views, etc.
-         */
         session: types.maybe(sessionModelType),
-        /**
-         * #property
-         */
         sessionPath: types.optional(types.string, ''),
-        /**
-         * #property
-         */
         assemblyManager: types.optional(assemblyManagerFactory(assemblyConfigSchema, pluginManager), {}),
     })
         .volatile(self => ({
@@ -41,43 +20,28 @@ export function BaseRootModelFactory({ pluginManager, jbrowseModelType, sessionM
         pluginManager,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setError(error) {
             self.error = error;
         },
-        /**
-         * #action
-         */
         setSession(sessionSnapshot) {
             self.session = cast(sessionSnapshot);
         },
-        /**
-         * #action
-         */
         setDefaultSession() {
             this.setSession(self.jbrowse.defaultSession);
         },
-        /**
-         * #action
-         */
         setSessionPath(path) {
             self.sessionPath = path;
         },
-        /**
-         * #action
-         */
         renameCurrentSession(newName) {
             if (self.session) {
-                const snapshot = JSON.parse(JSON.stringify(getSnapshot(self.session)));
-                snapshot.name = newName;
-                this.setSession(snapshot);
+                this.setSession({
+                    ...getSnapshot(self.session),
+                    name: newName,
+                });
             }
         },
     }));
 }
-/** Type guard for checking if something is a JB root model */
 export function isRootModel(thing) {
     return (isStateTreeNode(thing) &&
         'session' in thing &&

package/esm/RootModel/FormatAbout.d.ts

@@ -1,20 +1,10 @@
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 export declare function FormatAboutConfigSchemaFactory(): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot configuration.formatAbout.config
-     */
     config: {
         type: string;
         description: string;
         defaultValue: {};
         contextVariable: string[];
     };
-    /**
-     * #slot configuration.formatAbout.hideUris
-     */
     hideUris: {
         type: string;
         defaultValue: boolean;

package/esm/RootModel/FormatAbout.js

@@ -1,22 +1,12 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config FormatAbout
- * generally exists on the config.json or root config as configuration.formatAbout
- */
 export function FormatAboutConfigSchemaFactory() {
     return ConfigurationSchema('FormatAbout', {
-        /**
-         * #slot configuration.formatAbout.config
-         */
         config: {
             type: 'frozen',
             description: 'formats configuration object in about dialog',
             defaultValue: {},
             contextVariable: ['config'],
         },
-        /**
-         * #slot configuration.formatAbout.hideUris
-         */
         hideUris: {
             type: 'boolean',
             defaultValue: false,