@jbrowse/plugin-data-management 2.18.0 → 3.0.0

package/dist/UCSCTrackHub/ucscTrackHub.js

@@ -4,190 +4,166 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ucscAssemblies = void 0;
-exports.fetchGenomesFile = fetchGenomesFile;
-exports.fetchTrackDbFile = fetchTrackDbFile;
-exports.makeLoc = makeLoc;
-exports.makeLocAlt = makeLocAlt;
-exports.makeLoc2 = makeLoc2;
 exports.generateTracks = generateTracks;
-const ucsc_hub_1 = require("@gmod/ucsc-hub");
 const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
 const tracks_1 = require("@jbrowse/core/util/tracks");
-async function fetchGenomesFile(genomesLoc) {
-    const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
-    return new ucsc_hub_1.GenomesFile(genomesFileText);
-}
-async function fetchTrackDbFile(trackDbLoc) {
-    const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
-    return new ucsc_hub_1.TrackDbFile(text);
-}
-function makeLoc(first, base) {
-    return {
-        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
-        locationType: 'UriLocation',
-    };
-}
-function makeLocAlt(first, alt, base) {
-    return first ? makeLoc(first, base) : makeLoc(alt, base);
-}
-function makeLoc2(first, alt) {
-    return first
-        ? {
-            uri: first,
-            locationType: 'LocalPath',
-        }
-        : {
-            uri: alt,
-            locationType: 'UriLocation',
-        };
-}
-function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, }) {
+const util_2 = require("./util");
+function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }) {
+    const parentTrackKeys = new Set([
+        'superTrack',
+        'compositeTrack',
+        'container',
+        'view',
+    ]);
     return Object.entries(trackDb.data)
         .map(([trackName, track]) => {
         var _a;
-        const trackKeys = Object.keys(track);
-        const parentTrackKeys = new Set([
-            'superTrack',
-            'compositeTrack',
-            'container',
-            'view',
-        ]);
-        if (trackKeys.some(key => parentTrackKeys.has(key))) {
+        const { data } = track;
+        if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
             return undefined;
         }
-        const parentTracks = [];
-        let currentTrackName = trackName;
-        do {
-            currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
-            if (currentTrackName) {
-                currentTrackName = currentTrackName.split(' ')[0];
-                parentTracks.push(trackDb.data[currentTrackName]);
-            }
-        } while (currentTrackName);
-        parentTracks.reverse();
-        const categories = parentTracks
-            .map(p => p === null || p === void 0 ? void 0 : p.data.shortLabel)
-            .filter((f) => !!f);
-        const res = makeTrackConfig({
-            track: track,
-            categories,
-            trackDbLoc,
-            trackDb,
-            sequenceAdapter,
-        });
-        return {
-            ...res,
-            trackId: `ucsc-trackhub-${(0, util_1.objectHash)(res)}`,
-            assemblyNames: [assemblyName],
-        };
+        else {
+            const parentTracks = [];
+            let currentTrackName = trackName;
+            do {
+                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
+                if (currentTrackName) {
+                    currentTrackName = currentTrackName.split(' ')[0];
+                    parentTracks.push(trackDb.data[currentTrackName]);
+                }
+            } while (currentTrackName);
+            parentTracks.reverse();
+            return {
+                metadata: {
+                    ucscConfig: {
+                        ...track.data,
+                        ...(track.data.html
+                            ? {
+                                html: `<a href="${(0, util_2.resolve)(track.data.html, baseUrl)}">${track.data.html}</a>`,
+                            }
+                            : {}),
+                    },
+                },
+                category: [
+                    track.data.group,
+                    ...parentTracks
+                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
+                        .filter((f) => !!f),
+                ].filter(f => !!f),
+                ...makeTrackConfig({
+                    track,
+                    trackDbLoc,
+                    trackDb,
+                    sequenceAdapter,
+                }),
+            };
+        }
     })
-        .filter(util_1.notEmpty);
+        .filter(util_1.notEmpty)
+        .map(r => ({
+        ...r,
+        trackId: `ucsc-trackhub-${(0, util_1.objectHash)(r)}`,
+        assemblyNames: [assemblyName],
+    }));
 }
-function makeTrackConfig({ track, categories, trackDbLoc, trackDb, sequenceAdapter, }) {
+function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
     var _a;
-    const trackType = track.data.type || ((_a = trackDb.data[track.data.parent || '']) === null || _a === void 0 ? void 0 : _a.data.type) || '';
-    const name = track.data.shortLabel || '';
-    const bigDataUrl = track.data.bigDataUrl || '';
-    const bigDataIdx = track.data.bigDataIndex || '';
+    const { data } = track;
+    const parent = data.parent || '';
+    const bigDataUrl = data.bigDataUrl || '';
+    const bigDataIdx = data.bigDataIndex || '';
+    const trackType = data.type || ((_a = trackDb.data[parent]) === null || _a === void 0 ? void 0 : _a.data.type) || '';
+    const name = (data.shortLabel || '') + (bigDataUrl.includes('xeno') ? ' (xeno)' : '');
     const isUri = (0, util_1.isUriLocation)(trackDbLoc);
     let baseTrackType = trackType.split(' ')[0] || '';
     if (baseTrackType === 'bam' && bigDataUrl.toLowerCase().endsWith('cram')) {
         baseTrackType = 'cram';
     }
     const bigDataLocation = isUri
-        ? makeLoc(bigDataUrl, trackDbLoc)
-        : makeLoc2(bigDataUrl);
-    switch (baseTrackType) {
-        case 'bam':
-            return {
-                type: 'AlignmentsTrack',
-                name: track.data.longLabel,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BamAdapter',
-                    bamLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.bai`),
-                    },
-                },
-            };
-        case 'cram':
-            return {
-                type: 'AlignmentsTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'CramAdapter',
-                    cramLocation: bigDataLocation,
-                    craiLocation: isUri
-                        ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
-                        : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-                    sequenceAdapter,
-                },
-            };
-        case 'bigBarChart':
-        case 'bigBed':
-        case 'bigGenePred':
-        case 'bigChain':
-        case 'bigInteract':
-        case 'bigMaf':
-        case 'bigNarrowPeak':
-        case 'bigPsl':
-            return {
-                type: 'FeatureTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: bigDataLocation,
-                },
-            };
-        case 'bigWig':
-            return {
-                type: 'QuantitativeTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'BigWigAdapter',
-                    bigWigLocation: bigDataLocation,
-                },
-            };
-        case 'vcfTabix':
-            return {
-                type: 'VariantTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'VcfTabixAdapter',
-                    vcfGzLocation: bigDataLocation,
-                    index: {
-                        location: isUri
-                            ? makeLocAlt(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
-                            : makeLoc2(bigDataIdx, `${bigDataUrl}.tbi`),
-                    },
+        ? (0, util_2.makeLoc)(bigDataUrl, trackDbLoc)
+        : (0, util_2.makeLoc2)(bigDataUrl);
+    if (baseTrackType === 'bam') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BamAdapter',
+                bamLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.bai`, trackDbLoc)
+                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.bai`),
                 },
-            };
-        case 'hic':
-            return {
-                type: 'HicTrack',
-                name,
-                description: track.data.longLabel,
-                category: categories,
-                adapter: {
-                    type: 'HicAdapter',
-                    hicLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType === 'cram') {
+        return {
+            type: 'AlignmentsTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'CramAdapter',
+                cramLocation: bigDataLocation,
+                craiLocation: isUri
+                    ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
+                    : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.crai`),
+                sequenceAdapter,
+            },
+        };
+    }
+    else if (baseTrackType === 'bigWig') {
+        return {
+            type: 'QuantitativeTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigWigAdapter',
+                bigWigLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType.startsWith('big')) {
+        return {
+            type: 'FeatureTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'BigBedAdapter',
+                bigBedLocation: bigDataLocation,
+            },
+        };
+    }
+    else if (baseTrackType === 'vcfTabix') {
+        return {
+            type: 'VariantTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: bigDataLocation,
+                index: {
+                    location: isUri
+                        ? (0, util_2.makeLocAlt)(bigDataIdx, `${bigDataUrl}.tbi`, trackDbLoc)
+                        : (0, util_2.makeLoc2)(bigDataIdx, `${bigDataUrl}.tbi`),
                 },
-            };
-        default:
-            return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType, categories);
+            },
+        };
+    }
+    else if (baseTrackType === 'hic') {
+        return {
+            type: 'HicTrack',
+            name,
+            description: data.longLabel,
+            adapter: {
+                type: 'HicAdapter',
+                hicLocation: bigDataLocation,
+            },
+        };
+    }
+    else {
+        return (0, tracks_1.generateUnknownTrackConf)(name, baseTrackType);
     }
 }
 var ucscAssemblies_1 = require("./ucscAssemblies");

package/dist/UCSCTrackHub/util.d.ts

@@ -0,0 +1,22 @@
+import { GenomesFile, TrackDbFile } from '@gmod/ucsc-hub';
+import type { FileLocation } from '@jbrowse/core/util';
+export declare function fetchGenomesFile(genomesLoc: FileLocation): Promise<GenomesFile>;
+export declare function fetchTrackDbFile(trackDbLoc: FileLocation): Promise<TrackDbFile>;
+export declare function makeLoc(first: string, base: {
+    uri: string;
+    baseUri?: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLocAlt(first: string, alt: string, base: {
+    uri: string;
+}): {
+    uri: string;
+    locationType: string;
+};
+export declare function makeLoc2(first: string, alt?: string): {
+    uri: string | undefined;
+    locationType: string;
+};
+export declare function resolve(uri: string, baseUri: string): string;

package/dist/UCSCTrackHub/util.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.fetchGenomesFile = fetchGenomesFile;
+exports.fetchTrackDbFile = fetchTrackDbFile;
+exports.makeLoc = makeLoc;
+exports.makeLocAlt = makeLocAlt;
+exports.makeLoc2 = makeLoc2;
+exports.resolve = resolve;
+const ucsc_hub_1 = require("@gmod/ucsc-hub");
+const io_1 = require("@jbrowse/core/util/io");
+async function fetchGenomesFile(genomesLoc) {
+    const genomesFileText = await (0, io_1.openLocation)(genomesLoc).readFile('utf8');
+    return new ucsc_hub_1.GenomesFile(genomesFileText);
+}
+async function fetchTrackDbFile(trackDbLoc) {
+    const text = await (0, io_1.openLocation)(trackDbLoc).readFile('utf8');
+    return new ucsc_hub_1.TrackDbFile(text);
+}
+function makeLoc(first, base) {
+    return {
+        uri: new URL(first, new URL(base.uri, base.baseUri)).href,
+        locationType: 'UriLocation',
+    };
+}
+function makeLocAlt(first, alt, base) {
+    return first ? makeLoc(first, base) : makeLoc(alt, base);
+}
+function makeLoc2(first, alt) {
+    return first
+        ? {
+            uri: first,
+            locationType: 'LocalPath',
+        }
+        : {
+            uri: alt,
+            locationType: 'UriLocation',
+        };
+}
+function resolve(uri, baseUri) {
+    return new URL(uri, baseUri).href;
+}

package/dist/index.d.ts

@@ -3,14 +3,14 @@ import type PluginManager from '@jbrowse/core/PluginManager';
 declare const AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
     session: import("@jbrowse/core/util").AbstractSessionModel;
     onClose: () => void;
-}) => import("react").JSX.Element>;
+}) => import("react/jsx-runtime").JSX.Element>;
 export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
         AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
             session: import("@jbrowse/core/util").AbstractSessionModel;
             onClose: () => void;
-        }) => import("react").JSX.Element>;
+        }) => import("react/jsx-runtime").JSX.Element>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;

package/dist/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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 __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/esm/AddConnectionWidget/components/AddConnectionWidget.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
 declare const AddConnectionWidget: ({ model }: {
     model: unknown;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AddConnectionWidget;

package/esm/AddConnectionWidget/components/AddConnectionWidget.js

@@ -1,4 +1,5 @@
-import React, { useMemo, useState } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { useMemo, useState } from 'react';
 import { getEnv, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { isSessionWithConnections } from '@jbrowse/product-core';
 import { Button, Step, StepContent, StepLabel, Stepper } from '@mui/material';
@@ -30,38 +31,31 @@ const AddConnectionWidget = observer(function ({ model }) {
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
     const configModel = useMemo(() => connectionType === null || connectionType === void 0 ? void 0 : connectionType.configSchema.create({ connectionId }, getEnv(model)), [connectionId, connectionType, model]);
-    return (React.createElement("div", { className: classes.root },
-        React.createElement(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical" }, steps.map(label => (React.createElement(Step, { key: label },
-            React.createElement(StepLabel, null, label),
-            React.createElement(StepContent, null,
-                activeStep === 0 ? (React.createElement(ConnectionTypeSelect, { connectionTypeChoices: pluginManager.getConnectionElements(), connectionType: connectionType, setConnectionType: c => {
-                        setConnectionType(c);
-                        if (!c) {
-                            return;
-                        }
-                        setConnectionId(`${c.name}-${Date.now()}`);
-                    } })) : connectionType && configModel ? (React.createElement(ConfigureConnection, { connectionType: connectionType, model: configModel, session: session })) : null,
-                React.createElement("div", { className: classes.actionsContainer },
-                    React.createElement(Button, { disabled: activeStep === 0, onClick: () => {
-                            setActiveStep(activeStep - 1);
-                        }, className: classes.button }, "Back"),
-                    React.createElement(Button, { disabled: !((activeStep === 0 && connectionType) ||
-                            (activeStep === 1 && configModel)), variant: "contained", color: "primary", onClick: () => {
-                            if (activeStep === steps.length - 1) {
-                                if (configModel && isSessionWithConnections(session)) {
-                                    const conf = session.addConnectionConf(configModel);
-                                    session.makeConnection(conf);
-                                }
-                                else {
-                                    session.notify('No config model to add');
-                                }
-                                if (isSessionModelWithWidgets(session)) {
-                                    session.hideWidget(model);
-                                }
-                            }
-                            else {
-                                setActiveStep(activeStep + 1);
-                            }
-                        }, className: classes.button, "data-testid": "addConnectionNext" }, activeStep === steps.length - 1 ? 'Connect' : 'Next')))))))));
+    return (_jsx("div", { className: classes.root, children: _jsx(Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical", children: steps.map(label => (_jsxs(Step, { children: [_jsx(StepLabel, { children: label }), _jsxs(StepContent, { children: [activeStep === 0 ? (_jsx(ConnectionTypeSelect, { connectionTypeChoices: pluginManager.getConnectionElements(), connectionType: connectionType, setConnectionType: c => {
+                                    setConnectionType(c);
+                                    if (!c) {
+                                        return;
+                                    }
+                                    setConnectionId(`${c.name}-${Date.now()}`);
+                                } })) : connectionType && configModel ? (_jsx(ConfigureConnection, { connectionType: connectionType, model: configModel, session: session })) : null, _jsxs("div", { className: classes.actionsContainer, children: [_jsx(Button, { disabled: activeStep === 0, onClick: () => {
+                                            setActiveStep(activeStep - 1);
+                                        }, className: classes.button, children: "Back" }), _jsx(Button, { disabled: !((activeStep === 0 && connectionType) ||
+                                            (activeStep === 1 && configModel)), variant: "contained", color: "primary", onClick: () => {
+                                            if (activeStep === steps.length - 1) {
+                                                if (configModel && isSessionWithConnections(session)) {
+                                                    const conf = session.addConnectionConf(configModel);
+                                                    session.makeConnection(conf);
+                                                }
+                                                else {
+                                                    session.notify('No config model to add');
+                                                }
+                                                if (isSessionModelWithWidgets(session)) {
+                                                    session.hideWidget(model);
+                                                }
+                                            }
+                                            else {
+                                                setActiveStep(activeStep + 1);
+                                            }
+                                        }, className: classes.button, "data-testid": "addConnectionNext", children: activeStep === steps.length - 1 ? 'Connect' : 'Next' })] })] })] }, label))) }) }));
 });
 export default AddConnectionWidget;

package/esm/AddConnectionWidget/components/ConfigureConnection.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 import type { AbstractSessionModel } from '@jbrowse/core/util';
@@ -6,5 +5,5 @@ declare const ConfigureConnection: ({ connectionType, model, session, }: {
     connectionType: ConnectionType;
     model: AnyConfigurationModel;
     session: AbstractSessionModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ConfigureConnection;

package/esm/AddConnectionWidget/components/ConfigureConnection.js

@@ -1,10 +1,10 @@
-import React, { Suspense } from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
+import { Suspense } from 'react';
 import { LoadingEllipses } from '@jbrowse/core/ui';
 import { ConfigurationEditor } from '@jbrowse/plugin-config';
 import { observer } from 'mobx-react';
 const ConfigureConnection = observer(function ({ connectionType, model, session, }) {
     const ConfigEditorComponent = connectionType.configEditorComponent || ConfigurationEditor;
-    return (React.createElement(Suspense, { fallback: React.createElement(LoadingEllipses, null) },
-        React.createElement(ConfigEditorComponent, { model: { target: model }, session: session })));
+    return (_jsx(Suspense, { fallback: _jsx(LoadingEllipses, {}), children: _jsx(ConfigEditorComponent, { model: { target: model }, session: session }) }));
 });
 export default ConfigureConnection;

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
 declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
     connectionTypeChoices: ConnectionType[];
     connectionType?: ConnectionType;
     setConnectionType: (c?: ConnectionType) => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ConnectionTypeSelect;

package/esm/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -1,4 +1,5 @@
-import React, { useEffect } from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useEffect } from 'react';
 import OpenInNewIcon from '@mui/icons-material/OpenInNew';
 import { IconButton, MenuItem, TextField } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -9,11 +10,8 @@ const ConnectionTypeSelect = observer(function ConnectionTypeSelect({ connection
             setConnectionType(firstChoice);
         }
     }, [connectionType, firstChoice, setConnectionType]);
-    return (React.createElement("form", { autoComplete: "off" }, connectionType ? (React.createElement(TextField, { value: connectionType.name, label: "connectionType", helperText: connectionType.description ? (React.createElement(React.Fragment, null,
-            connectionType.description,
-            connectionType.url ? (React.createElement(IconButton, { href: connectionType.url, rel: "noopener noreferrer", target: "_blank" },
-                React.createElement(OpenInNewIcon, null))) : null)) : null, select: true, fullWidth: true, onChange: event => {
-            setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value));
-        }, variant: "outlined" }, connectionTypeChoices.map(c => (React.createElement(MenuItem, { key: c.name, value: c.name }, c.displayName || c.name))))) : null));
+    return (_jsx("form", { autoComplete: "off", children: connectionType ? (_jsx(TextField, { value: connectionType.name, label: "connectionType", helperText: connectionType.description ? (_jsxs(_Fragment, { children: [connectionType.description, connectionType.url ? (_jsx(IconButton, { href: connectionType.url, rel: "noopener noreferrer", target: "_blank", children: _jsx(OpenInNewIcon, {}) })) : null] })) : null, select: true, fullWidth: true, onChange: event => {
+                setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value));
+            }, variant: "outlined", children: connectionTypeChoices.map(c => (_jsx(MenuItem, { value: c.name, children: c.displayName || c.name }, c.name))) })) : null }));
 });
 export default ConnectionTypeSelect;

package/esm/AddTrackWidget/components/AddTrackStatusMessage.d.ts

@@ -0,0 +1,9 @@
+export default function StatusMessage({ trackAdapter, trackType, }: {
+    trackAdapter: {
+        type: string;
+        subadapter?: {
+            type: string;
+        };
+    };
+    trackType: string;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/AddTrackStatusMessage.js

@@ -0,0 +1,13 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Typography } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(theme => ({
+    spacing: {
+        marginBottom: theme.spacing(3),
+    },
+}));
+export default function StatusMessage({ trackAdapter, trackType, }) {
+    const { classes } = useStyles();
+    const { type, subadapter } = trackAdapter;
+    return type === 'SNPCoverageAdapter' ? (_jsxs(Typography, { className: classes.spacing, children: ["Selected ", _jsx("code", { children: trackType }), ". Using adapter ", _jsx("code", { children: type }), " with subadapter ", _jsx("code", { children: subadapter === null || subadapter === void 0 ? void 0 : subadapter.type }), ". Please enter a track name and, if necessary, update the track type."] })) : (_jsxs(Typography, { className: classes.spacing, children: ["Using adapter ", _jsx("code", { children: type }), " and guessing track type", ' ', _jsx("code", { children: trackType }), ". Please enter a track name and, if necessary, update the track type."] }));
+}

package/esm/AddTrackWidget/components/AddTrackUnknownAdapterPrompt.d.ts

@@ -0,0 +1,4 @@
+import type { AddTrackModel } from '../model';
+export default function UnknownAdapterPrompt({ model, }: {
+    model: AddTrackModel;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/AddTrackUnknownAdapterPrompt.js

@@ -0,0 +1,13 @@
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { Link, Typography } from '@mui/material';
+import { makeStyles } from 'tss-react/mui';
+import TrackAdapterSelector from './TrackAdapterSelector';
+const useStyles = makeStyles()(theme => ({
+    spacing: {
+        marginBottom: theme.spacing(3),
+    },
+}));
+export default function UnknownAdapterPrompt({ model, }) {
+    const { classes } = useStyles();
+    return (_jsxs(_Fragment, { children: [_jsxs(Typography, { className: classes.spacing, children: ["JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can", ' ', _jsx(Link, { href: "https://github.com/GMOD/jbrowse-components/releases", target: "_blank", rel: "noopener noreferrer", children: "check for new releases" }), ' ', "of JBrowse to see if they support this data type or", ' ', _jsx(Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer", children: "file an issue" }), ' ', "and add a feature request for this data type."] }), _jsx(TrackAdapterSelector, { model: model })] }));
+}