@jbrowse/product-core 2.11.1 → 2.12.0

package/dist/ui/AboutDialogContents.d.ts

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

package/dist/ui/AboutDialogContents.js

@@ -27,6 +27,7 @@ var __importDefault = (this && this.__importDefault) || function (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");
@@ -35,10 +36,14 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const BaseFeatureDetail_1 = require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail");
 const FileInfoPanel_1 = __importDefault(require("./FileInfoPanel"));
+const RefNameInfoDialog_1 = __importDefault(require("./RefNameInfoDialog"));
 const useStyles = (0, mui_1.makeStyles)()({
     content: {
         minWidth: 800,
     },
+    button: {
+        float: 'right',
+    },
 });
 function removeAttr(obj, attr) {
     for (const prop in obj) {
@@ -51,11 +56,12 @@ function removeAttr(obj, attr) {
     }
     return obj;
 }
-function AboutContents({ config, }) {
+const AboutDialogContents = (0, mobx_react_1.observer)(function ({ config, }) {
     const [copied, setCopied] = (0, react_1.useState)(false);
     const conf = (0, configuration_1.readConfObject)(config);
     const session = (0, util_1.getSession)(config);
     const { classes } = useStyles();
+    const [showRefNames, setShowRefNames] = (0, react_1.useState)(false);
     const hideUris = (0, configuration_1.getConf)(session, ['formatAbout', 'hideUris']) ||
         (0, configuration_1.readConfObject)(config, ['formatAbout', 'hideUris']);
     const { pluginManager } = (0, util_1.getEnv)(session);
@@ -69,15 +75,18 @@ function AboutContents({ config, }) {
     const ExtraPanel = pluginManager.evaluateExtensionPoint('Core-extraAboutPanel', null, { session, config });
     return (react_1.default.createElement("div", { className: classes.content },
         react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: "Configuration" },
-            !hideUris ? (react_1.default.createElement(material_1.Button, { variant: "contained", style: { float: 'right' }, 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,
+            !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(BaseFeatureDetail_1.Attributes, { attributes: confPostExt, omit: ['displays', 'baseUri', 'refNames', 'formatAbout'], hideUris: hideUris })),
         ExtraPanel ? (react_1.default.createElement(BaseFeatureDetail_1.BaseCard, { title: ExtraPanel.name },
             react_1.default.createElement(ExtraPanel.Component, { config: config }))) : null,
-        react_1.default.createElement(FileInfoPanel_1.default, { config: config })));
-}
-exports.default = AboutContents;
+        react_1.default.createElement(FileInfoPanel_1.default, { config: config }),
+        showRefNames ? (react_1.default.createElement(RefNameInfoDialog_1.default, { config: config, onClose: () => setShowRefNames(false) })) : null));
+});
+exports.default = AboutDialogContents;

package/dist/ui/RefNameInfoDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const RefNameInfoDialog: ({ config, onClose, }: {
+    config: AnyConfigurationModel;
+    onClose: () => void;
+}) => React.JSX.Element;
+export default RefNameInfoDialog;

package/dist/ui/RefNameInfoDialog.js

@@ -0,0 +1,110 @@
+"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 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 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: {
+        minWidth: 800,
+    },
+    refNames: {
+        maxHeight: 300,
+        width: '100%',
+        overflow: 'auto',
+        flexGrow: 1,
+        background: theme.palette.background.default,
+    },
+}));
+const RefNameInfoDialog = (0, mobx_react_1.observer)(function ({ config, onClose, }) {
+    const [error, setError] = (0, react_1.useState)();
+    const [refNames, setRefNames] = (0, react_1.useState)();
+    const [copied, setCopied] = (0, react_1.useState)(false);
+    const { classes } = useStyles();
+    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 {
+                const map = await Promise.all([...new Set((0, tracks_1.getConfAssemblyNames)(config))].map(async (assemblyName) => {
+                    const adapterConfig = (0, configuration_1.readConfObject)(config, 'adapter');
+                    return [
+                        assemblyName,
+                        (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
+                            adapterConfig,
+                            // hack for synteny adapters
+                            regions: [{ assemblyName }],
+                        })),
+                    ];
+                }));
+                setRefNames(Object.fromEntries(map));
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [config, rpcManager]);
+    const names = refNames ? Object.entries(refNames) : [];
+    const result = names
+        .flatMap(([assemblyName, refNames]) => {
+        return [
+            `--- ${assemblyName} ---`,
+            ...refNames.slice(0, MAX_REF_NAMES),
+            `${refNames.length > MAX_REF_NAMES
+                ? `\nToo many refNames to show in browser for ${assemblyName}, use "Copy ref names" button to copy to clipboard`
+                : ''}`,
+        ];
+    })
+        .filter(f => !!f)
+        .join('\n');
+    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose },
+        react_1.default.createElement(material_1.DialogContent, { className: classes.container }, error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${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))))));
+});
+exports.default = RefNameInfoDialog;

package/esm/ui/AboutDialogContents.d.ts

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

package/esm/ui/AboutDialogContents.js

@@ -1,4 +1,5 @@
 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';
@@ -7,10 +8,14 @@ import { getConf, readConfObject, } from '@jbrowse/core/configuration';
 import { getSession, getEnv } from '@jbrowse/core/util';
 import { BaseCard, Attributes, } from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail';
 import FileInfoPanel from './FileInfoPanel';
+import RefNameInfoDialog from './RefNameInfoDialog';
 const useStyles = makeStyles()({
     content: {
         minWidth: 800,
     },
+    button: {
+        float: 'right',
+    },
 });
 function removeAttr(obj, attr) {
     for (const prop in obj) {
@@ -23,11 +28,12 @@ function removeAttr(obj, attr) {
     }
     return obj;
 }
-export default function AboutContents({ config, }) {
+const AboutDialogContents = observer(function ({ config, }) {
     const [copied, setCopied] = useState(false);
     const conf = readConfObject(config);
     const session = getSession(config);
     const { classes } = useStyles();
+    const [showRefNames, setShowRefNames] = useState(false);
     const hideUris = getConf(session, ['formatAbout', 'hideUris']) ||
         readConfObject(config, ['formatAbout', 'hideUris']);
     const { pluginManager } = getEnv(session);
@@ -41,14 +47,18 @@ export default function AboutContents({ 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(Button, { variant: "contained", style: { float: 'right' }, 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,
+            !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 })));
-}
+        React.createElement(FileInfoPanel, { config: config }),
+        showRefNames ? (React.createElement(RefNameInfoDialog, { config: config, onClose: () => setShowRefNames(false) })) : null));
+});
+export default AboutDialogContents;

package/esm/ui/RefNameInfoDialog.d.ts

@@ -0,0 +1,7 @@
+import React from 'react';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const RefNameInfoDialog: ({ config, onClose, }: {
+    config: AnyConfigurationModel;
+    onClose: () => void;
+}) => React.JSX.Element;
+export default RefNameInfoDialog;

package/esm/ui/RefNameInfoDialog.js

@@ -0,0 +1,82 @@
+import React, { useState, useEffect } from 'react';
+import { Button, DialogContent, Typography } from '@mui/material';
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { Dialog, LoadingEllipses } from '@jbrowse/core/ui';
+import { getSession } from '@jbrowse/core/util';
+import { getConfAssemblyNames } from '@jbrowse/core/util/tracks';
+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: {
+        minWidth: 800,
+    },
+    refNames: {
+        maxHeight: 300,
+        width: '100%',
+        overflow: 'auto',
+        flexGrow: 1,
+        background: theme.palette.background.default,
+    },
+}));
+const RefNameInfoDialog = observer(function ({ config, onClose, }) {
+    const [error, setError] = useState();
+    const [refNames, setRefNames] = useState();
+    const [copied, setCopied] = useState(false);
+    const { classes } = useStyles();
+    const session = getSession(config);
+    const { rpcManager } = session;
+    useEffect(() => {
+        // eslint-disable-next-line @typescript-eslint/no-floating-promises
+        ;
+        (async () => {
+            try {
+                const map = await Promise.all([...new Set(getConfAssemblyNames(config))].map(async (assemblyName) => {
+                    const adapterConfig = readConfObject(config, 'adapter');
+                    return [
+                        assemblyName,
+                        (await rpcManager.call(config.trackId, 'CoreGetRefNames', {
+                            adapterConfig,
+                            // hack for synteny adapters
+                            regions: [{ assemblyName }],
+                        })),
+                    ];
+                }));
+                setRefNames(Object.fromEntries(map));
+            }
+            catch (e) {
+                console.error(e);
+                setError(e);
+            }
+        })();
+    }, [config, rpcManager]);
+    const names = refNames ? Object.entries(refNames) : [];
+    const result = names
+        .flatMap(([assemblyName, refNames]) => {
+        return [
+            `--- ${assemblyName} ---`,
+            ...refNames.slice(0, MAX_REF_NAMES),
+            `${refNames.length > MAX_REF_NAMES
+                ? `\nToo many refNames to show in browser for ${assemblyName}, use "Copy ref names" button to copy to clipboard`
+                : ''}`,
+        ];
+    })
+        .filter(f => !!f)
+        .join('\n');
+    return (React.createElement(Dialog, { open: true, title: "Reference sequence names used in track", onClose: onClose },
+        React.createElement(DialogContent, { className: classes.container }, error ? (React.createElement(Typography, { color: "error" }, `${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))))));
+});
+export default RefNameInfoDialog;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/product-core",
-  "version": "2.11.1",
+  "version": "2.12.0",
   "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": "^2.11.1",
+    "@jbrowse/core": "^2.12.0",
     "@mui/icons-material": "^5.0.0",
     "@mui/material": "^5.10.17",
     "copy-to-clipboard": "^3.3.1",
@@ -63,5 +63,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "11b28d66d782eb06f92ccb993108bb6c3c82819e"
+  "gitHead": "935f2602d29abc737bb1f493a922b6218d023ae2"
 }