@jbrowse/product-core 2.17.0 → 3.0.0

package/esm/Session/Tracks.js

@@ -1,33 +1,18 @@
 import { types } from 'mobx-state-tree';
 import { BaseSessionModel, isBaseSession } from './BaseSession';
 import { ReferenceManagementSessionMixin } from './ReferenceManagement';
-/**
- * #stateModel TracksManagerSessionMixin
- * composed of
- * - BaseSessionModel
- * - ReferenceManagementSessionMixin
- */
 export function TracksManagerSessionMixin(pluginManager) {
     return types
         .compose('TracksManagerSessionMixin', BaseSessionModel(pluginManager), 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 = {};
@@ -42,7 +27,6 @@ export function TracksManagerSessionMixin(pluginManager) {
         },
     }));
 }
-/** Type guard for SessionWithTracks */
 export function isSessionWithTracks(thing) {
     return isBaseSession(thing) && 'tracks' in thing;
 }

package/esm/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/esm/rpcWorker.js

@@ -1,10 +1,7 @@
-import RpcServer from 'librpc-web-mod';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { remoteAbortRpcHandler } from '@jbrowse/core/rpc/remoteAbortSignals';
 import PluginLoader from '@jbrowse/core/PluginLoader';
+import PluginManager from '@jbrowse/core/PluginManager';
+import RpcServer from 'librpc-web-mod';
 import { serializeError } from '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) {
@@ -19,7 +16,6 @@ function receiveConfiguration() {
     return configurationP;
 }
 async function getPluginManager(corePlugins, opts) {
-    // Load runtime plugins
     const config = await receiveConfiguration();
     const pluginLoader = new PluginLoader(config.plugins, opts).installGlobalReExports(self);
     return new PluginManager([
@@ -35,7 +31,6 @@ function wrapForRpc(func) {
         return func({
             ...args,
             statusCallback: (message) => {
-                // @ts-expect-error
                 self.rpcServer.emit(channel, message);
             },
         }, rpcDriverClassName);
@@ -47,19 +42,10 @@ export 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 RpcServer.Server({
-            ...rpcConfig,
-            ...remoteAbortRpcHandler(),
-            ping: async () => {
-                // the ping method is required by the worker driver for checking the
-                // health of the worker
-            },
-        });
+        self.rpcServer = new RpcServer.Server(rpcConfig);
         postMessage({ message: 'ready' });
     }
     catch (e) {
         postMessage({ message: 'error', error: serializeError(e) });
     }
-    /* do nothing */
 }

package/esm/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/esm/ui/AboutDialog.js

@@ -1,6 +1,6 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import Dialog from '@jbrowse/core/ui/Dialog';
-import { getSession, getEnv } from '@jbrowse/core/util';
+import { getEnv, getSession } from '@jbrowse/core/util';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 import AboutContents from './AboutDialogContents';
 export function AboutDialog({ config, handleClose, }) {
@@ -8,6 +8,5 @@ export function AboutDialog({ config, handleClose, }) {
     const trackName = getTrackName(config, session);
     const { pluginManager } = getEnv(session);
     const AboutComponent = pluginManager.evaluateExtensionPoint('Core-replaceAbout', AboutContents, { session, config });
-    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl" },
-        React.createElement(AboutComponent, { config: config })));
+    return (_jsx(Dialog, { open: true, onClose: handleClose, title: trackName, maxWidth: "xl", children: _jsx(AboutComponent, { config: config }) }));
 }

package/esm/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/esm/ui/AboutDialogContents.js

@@ -1,14 +1,13 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import clone from 'clone';
-import copy from 'copy-to-clipboard';
-import { Button } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getSession, getEnv } from '@jbrowse/core/util';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-// locals
+import { getConf, readConfObject } from '@jbrowse/core/configuration';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import { Button } from '@mui/material';
+import copy from 'copy-to-clipboard';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 import FileInfoPanel from './FileInfoPanel';
 import RefNameInfoDialog from './RefNameInfoDialog';
 const useStyles = makeStyles()({
@@ -47,26 +46,17 @@ const AboutDialogContents = observer(function ({ config, }) {
         },
     }, { session, config });
     const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
-    return (React.createElement("div", { className: classes.content },
-        React.createElement(BaseCard, { title: "Configuration" },
-            !hideUris ? (React.createElement("span", { className: classes.button },
-                React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => {
-                        setShowRefNames(true);
-                    } }, "Show ref names"),
-                React.createElement(Button, { variant: "contained", onClick: () => {
-                        const snap = removeAttr(clone(conf), 'baseUri');
-                        copy(JSON.stringify(snap, null, 2));
-                        setCopied(true);
-                        setTimeout(() => {
-                            setCopied(false);
-                        }, 1000);
-                    } }, copied ? 'Copied to clipboard!' : 'Copy config'))) : null,
-            React.createElement(Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
-        ExtraPanel ? (React.createElement(BaseCard, { title: ExtraPanel.name },
-            React.createElement(ExtraPanel.Component, { config: config }))) : null,
-        React.createElement(FileInfoPanel, { config: config }),
-        showRefNames ? (React.createElement(RefNameInfoDialog, { config: config, onClose: () => {
-                setShowRefNames(false);
-            } })) : null));
+    return (_jsxs("div", { className: classes.content, children: [_jsxs(BaseCard, { title: "Configuration", children: [!hideUris ? (_jsxs("span", { className: classes.button, children: [_jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                                    setShowRefNames(true);
+                                }, children: "Show ref names" }), _jsx(Button, { variant: "contained", onClick: () => {
+                                    const snap = removeAttr(structuredClone(conf), 'baseUri');
+                                    copy(JSON.stringify(snap, null, 2));
+                                    setCopied(true);
+                                    setTimeout(() => {
+                                        setCopied(false);
+                                    }, 1000);
+                                }, children: copied ? 'Copied to clipboard!' : 'Copy config' })] })) : null, _jsx(Attributes, { attributes: confPostExt.config, omit: ['displays', 'baseUri', 'refNames', 'formatAbout', 'metadata'], hideUris: hideUris })] }), confPostExt.config.metadata ? (_jsx(BaseCard, { title: "Metadata", children: _jsx(Attributes, { attributes: confPostExt.config.metadata, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris }) })) : null, ExtraPanel ? (_jsx(BaseCard, { title: ExtraPanel.name, children: _jsx(ExtraPanel.Component, { config: config }) })) : null, _jsx(FileInfoPanel, { config: config }), showRefNames ? (_jsx(RefNameInfoDialog, { config: config, onClose: () => {
+                    setShowRefNames(false);
+                } })) : null] }));
 });
 export default AboutDialogContents;

package/esm/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/esm/ui/FileInfoPanel.js

@@ -1,16 +1,16 @@
-import React, { useState, useEffect } from 'react';
-import { readConfObject, } from '@jbrowse/core/configuration';
-import { getSession } from '@jbrowse/core/util';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
 import Attributes from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/Attributes';
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
 export default function FileInfoPanel({ config, }) {
     const [error, setError] = useState();
     const [info, setInfo] = useState();
     const session = getSession(config);
     const { rpcManager } = session;
     useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -33,5 +33,5 @@ export default function FileInfoPanel({ config, }) {
                 .replaceAll('>', '&gt;')}</pre>`,
         }
         : info || {};
-    return (React.createElement(BaseCard, { title: "File info" }, error ? (React.createElement(ErrorMessage, { error: error })) : info === undefined ? (React.createElement(LoadingEllipses, { message: "Loading file data" })) : (React.createElement(Attributes, { attributes: details }))));
+    return (_jsx(BaseCard, { title: "File info", children: error ? (_jsx(ErrorMessage, { error: error })) : info === undefined ? (_jsx(LoadingEllipses, { message: "Loading file data" })) : (_jsx(Attributes, { attributes: details })) }));
 }

package/esm/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/esm/ui/RefNameInfoDialog.js

@@ -1,12 +1,13 @@
-import React, { useState, useEffect } from 'react';
-import { Button, DialogContent } from '@mui/material';
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect, useState } from 'react';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui';
 import { getSession } from '@jbrowse/core/util';
 import { getConfAssemblyNames } from '@jbrowse/core/util/tracks';
+import { Button, DialogContent } from '@mui/material';
+import copy from 'copy-to-clipboard';
 import { observer } from 'mobx-react';
 import { makeStyles } from 'tss-react/mui';
-import copy from 'copy-to-clipboard';
 const MAX_REF_NAMES = 10000;
 const useStyles = makeStyles()(theme => ({
     container: {
@@ -26,7 +27,6 @@ const RefNameInfoDialog = observer(function ({ config, onClose, }) {
     const [copied, setCopied] = useState(false);
     const { rpcManager } = getSession(config);
     useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -36,7 +36,6 @@ const RefNameInfoDialog = observer(function ({ config, onClose, }) {
                         assemblyName,
                         (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
                             adapterConfig,
-                            // hack for synteny adapters
                             regions: [
                                 {
                                     assemblyName,
@@ -66,21 +65,18 @@ const RefNameInfoDialog = observer(function ({ config, onClose, }) {
     })
         .filter(f => !!f)
         .join('\n');
-    return (React.createElement(Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl" },
-        React.createElement(DialogContent, { className: classes.container }, error ? (React.createElement(ErrorMessage, { error: error })) : refNames === undefined ? (React.createElement(LoadingEllipses, { message: "Loading refNames" })) : (React.createElement(React.Fragment, null,
-            React.createElement(Button, { variant: "contained", onClick: () => {
-                    copy(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.createElement("pre", { className: classes.refNames }, result))))));
+    return (_jsx(Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose, maxWidth: "xl", children: _jsx(DialogContent, { className: classes.container, children: error ? (_jsx(ErrorMessage, { error: error })) : refNames === undefined ? (_jsx(LoadingEllipses, { message: "Loading refNames" })) : (_jsxs(_Fragment, { children: [_jsx(Button, { variant: "contained", onClick: () => {
+                            copy(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' }), _jsx("pre", { className: classes.refNames, children: result })] })) }) }));
 });
 export default RefNameInfoDialog;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "sideEffects": false,
   "description": "JBrowse 2 code shared between products but not used by plugins",
   "keywords": [
@@ -43,7 +43,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.17.0",
+    "@jbrowse/core": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "copy-to-clipboard": "^3.3.1",
@@ -62,5 +62,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }