@jbrowse/plugin-data-management 2.17.0 → 3.0.0

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

@@ -1,20 +1,20 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
-declare const AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-    rootModel: any;
-    onClose: (arg: boolean) => void;
-}) => import("react").JSX.Element>;
+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-runtime").JSX.Element>;
 export default class DataManagementPlugin extends Plugin {
     name: string;
     exports: {
-        AssemblyManager: import("react").LazyExoticComponent<({ rootModel, onClose, }: {
-            rootModel: any;
-            onClose: (arg: boolean) => void;
-        }) => import("react").JSX.Element>;
+        AssemblyManager: import("react").LazyExoticComponent<({ session, onClose, }: {
+            session: import("@jbrowse/core/util").AbstractSessionModel;
+            onClose: () => void;
+        }) => import("react/jsx-runtime").JSX.Element>;
     };
     install(pluginManager: PluginManager): void;
     configure(_pluginManager: PluginManager): void;
 }
 export { AssemblyManager };
-export { type AddTrackModel } from './AddTrackWidget/model';
-export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
+export type { AddTrackModel } from './AddTrackWidget/model';
+export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';

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 };
 };
@@ -29,11 +39,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.AssemblyManager = void 0;
 const react_1 = require("react");
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const ucsc_trackhub_1 = __importDefault(require("./ucsc-trackhub"));
-const AddTrackWidget_1 = __importDefault(require("./AddTrackWidget"));
 const AddConnectionWidget_1 = __importDefault(require("./AddConnectionWidget"));
-const PluginStoreWidget_1 = __importDefault(require("./PluginStoreWidget"));
+const AddTrackWidget_1 = __importDefault(require("./AddTrackWidget"));
 const HierarchicalTrackSelectorWidget_1 = __importDefault(require("./HierarchicalTrackSelectorWidget"));
+const PluginStoreWidget_1 = __importDefault(require("./PluginStoreWidget"));
+const UCSCTrackHub_1 = __importDefault(require("./UCSCTrackHub"));
 const AssemblyManager = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AssemblyManager'))));
 exports.AssemblyManager = AssemblyManager;
 class DataManagementPlugin extends Plugin_1.default {
@@ -45,7 +55,7 @@ class DataManagementPlugin extends Plugin_1.default {
         };
     }
     install(pluginManager) {
-        (0, ucsc_trackhub_1.default)(pluginManager);
+        (0, UCSCTrackHub_1.default)(pluginManager);
         (0, AddTrackWidget_1.default)(pluginManager);
         (0, HierarchicalTrackSelectorWidget_1.default)(pluginManager);
         (0, AddConnectionWidget_1.default)(pluginManager);

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

@@ -1,12 +1,12 @@
-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';
-import { getSession, getEnv, isSessionModelWithWidgets, } from '@jbrowse/core/util';
-import { makeStyles } from 'tss-react/mui';
 import { observer } from 'mobx-react';
-// locals
+import { makeStyles } from 'tss-react/mui';
 import ConfigureConnection from './ConfigureConnection';
 import ConnectionTypeSelect from './ConnectionTypeSelect';
-import { isSessionWithConnections } from '@jbrowse/product-core';
 const useStyles = makeStyles()(theme => ({
     root: {
         marginTop: theme.spacing(1),
@@ -30,40 +30,32 @@ const AddConnectionWidget = observer(function ({ model }) {
     const { classes } = useStyles();
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
-    // useMemo is needed for react@18+mobx-react@9, previous code called configScema.create directly in a setConfigModel useState hook setter but this caused infinite loop
     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

@@ -1,10 +1,9 @@
-import React from 'react';
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { AbstractSessionModel } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
 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 { observer } from 'mobx-react';
-import { ConfigurationEditor } from '@jbrowse/plugin-config';
+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 { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+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

@@ -1,8 +1,8 @@
-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';
-// icons
-import OpenInNewIcon from '@mui/icons-material/OpenInNew';
 const ConnectionTypeSelect = observer(function ConnectionTypeSelect({ connectionTypeChoices, connectionType, setConnectionType, }) {
     const firstChoice = connectionTypeChoices[0];
     useEffect(() => {
@@ -10,11 +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/AddConnectionWidget/index.d.ts

@@ -1,2 +1,2 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function AddConnectionWidgetF(pluginManager: PluginManager): void;

package/esm/AddConnectionWidget/index.js

@@ -1,6 +1,6 @@
+import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import { lazy } from 'react';
 import stateModel from './model';
 const configSchema = ConfigurationSchema('AddConnectionWidget', {});
 export default function AddConnectionWidgetF(pluginManager) {

package/esm/AddConnectionWidget/model.js

@@ -1,5 +1,5 @@
-import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
 export default types.model('AddConnectionModel', {
     id: ElementId,
     type: types.literal('AddConnectionWidget'),

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 })] }));
+}

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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const AddTrackSelector: ({ model, }: {
     model: AddTrackModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AddTrackSelector;

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -1,7 +1,8 @@
-import React, { Suspense, useState } from 'react';
-import { observer } from 'mobx-react';
-import { FormControl, FormHelperText, Select, MenuItem } from '@mui/material';
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { Suspense, useState } from 'react';
 import { getEnv } from '@jbrowse/core/util';
+import { FormControl, FormHelperText, MenuItem, Select } from '@mui/material';
+import { observer } from 'mobx-react';
 import DefaultAddTrackWorkflow from './DefaultAddTrackWorkflow';
 import PasteConfigWorkflow from './PasteConfigWorkflow';
 const AddTrackSelector = observer(function ({ model, }) {
@@ -13,16 +14,10 @@ const AddTrackSelector = observer(function ({ model, }) {
             .pluginManager.getAddTrackWorkflowElements()
             .map(w => [w.name, w.ReactComponent])),
     };
-    // make sure the selected value is in the list
     const val2 = ComponentMap[val] ? val : 'Default add track workflow';
     const Component = ComponentMap[val2];
-    return (React.createElement(React.Fragment, null,
-        React.createElement(FormControl, null,
-            React.createElement(Select, { value: val2, onChange: event => {
-                    setVal(event.target.value);
-                } }, Object.keys(ComponentMap).map(e => (React.createElement(MenuItem, { key: e, value: e }, e)))),
-            React.createElement(FormHelperText, null, "Type of add track workflow")),
-        React.createElement(Suspense, { fallback: null },
-            React.createElement(Component, { model: model }))));
+    return (_jsxs(_Fragment, { children: [_jsxs(FormControl, { children: [_jsx(Select, { value: val2, onChange: event => {
+                            setVal(event.target.value);
+                        }, children: Object.keys(ComponentMap).map(e => (_jsx(MenuItem, { value: e, children: e }, e))) }), _jsx(FormHelperText, { children: "Type of add track workflow" })] }), _jsx(Suspense, { fallback: null, children: _jsx(Component, { model: model }) })] }));
 });
 export default AddTrackSelector;

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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const ConfirmTrack: ({ model, }: {
     model: AddTrackModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ConfirmTrack;

package/esm/AddTrackWidget/components/ConfirmTrack.js

@@ -1,51 +1,22 @@
-import React, { useEffect, useState } from 'react';
-import { Checkbox, FormControl, FormControlLabel, Link, TextField, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { isSupportedIndexingAdapter, getSession, isElectron, } from '@jbrowse/core/util';
-import { observer } from 'mobx-react';
-import { UNKNOWN } from '@jbrowse/core/util/tracks';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Suspense, useEffect, useState } from 'react';
 import { AssemblySelector } from '@jbrowse/core/ui';
+import { getEnv, getSession, isElectron, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
+import { UNKNOWN } from '@jbrowse/core/util/tracks';
+import { Checkbox, FormControl, FormControlLabel, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+import StatusMessage from './AddTrackStatusMessage';
+import UnknownAdapterPrompt from './AddTrackUnknownAdapterPrompt';
 import TextIndexingConfig from './TextIndexingConfig';
-import TrackTypeSelector from './TrackTypeSelector';
 import TrackAdapterSelector from './TrackAdapterSelector';
+import TrackTypeSelector from './TrackTypeSelector';
+import Unsupported from './Unsupported';
 const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
     },
 }));
-function StatusMessage({ trackAdapter, trackType, }) {
-    const { classes } = useStyles();
-    const { type, subadapter } = trackAdapter;
-    return type === 'SNPCoverageAdapter' ? (React.createElement(Typography, { className: classes.spacing },
-        "Selected ",
-        React.createElement("code", null, trackType),
-        ". Using adapter ",
-        React.createElement("code", null, type),
-        " with subadapter ",
-        React.createElement("code", null, subadapter === null || subadapter === void 0 ? void 0 : subadapter.type),
-        ". Please enter a track name and, if necessary, update the track type.")) : (React.createElement(Typography, { className: classes.spacing },
-        "Using adapter ",
-        React.createElement("code", null, type),
-        " and guessing track type",
-        ' ',
-        React.createElement("code", null, trackType),
-        ". Please enter a track name and, if necessary, update the track type."));
-}
-function UnknownAdapterPrompt({ model }) {
-    const { classes } = useStyles();
-    return (React.createElement(React.Fragment, null,
-        React.createElement(Typography, { className: classes.spacing },
-            "JBrowse was not able to guess the adapter type for this data, but it may be in the list below. If not, you can",
-            ' ',
-            React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/releases", target: "_blank", rel: "noopener noreferrer" }, "check for new releases"),
-            ' ',
-            "of JBrowse to see if they support this data type or",
-            ' ',
-            React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer" }, "file an issue"),
-            ' ',
-            "and add a feature request for this data type."),
-        React.createElement(TrackAdapterSelector, { model: model })));
-}
 const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
     const { classes } = useStyles();
     const [check, setCheck] = useState(true);
@@ -57,48 +28,41 @@ const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
         }
     }, [adapterHint, trackAdapter, trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type, model]);
     if (unsupported) {
-        return (React.createElement(Typography, { className: classes.spacing },
-            "This version of JBrowse cannot display data of this type. It is possible, however, that there is a newer version that can display them. You can",
-            ' ',
-            React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/releases", target: "_blank", rel: "noopener noreferrer" }, "check for new releases"),
-            ' ',
-            "of JBrowse or",
-            ' ',
-            React.createElement(Link, { href: "https://github.com/GMOD/jbrowse-components/issues/new", target: "_blank", rel: "noopener noreferrer" }, "file an issue"),
-            ' ',
-            "and add a feature request for this data type."));
+        return _jsx(Unsupported, {});
     }
-    if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
-        return React.createElement(UnknownAdapterPrompt, { model: model });
+    else if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
+        return _jsx(UnknownAdapterPrompt, { model: model });
     }
-    if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
-        return React.createElement(Typography, null, "Could not recognize this data type.");
+    else if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
+        return _jsx(Typography, { children: "Could not recognize this data type." });
     }
-    const supportedForIndexing = isSupportedIndexingAdapter(trackAdapter.type);
-    return (React.createElement("div", null,
-        React.createElement(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType }),
-        warningMessage ? (React.createElement(Typography, { style: { color: 'orange' } }, warningMessage)) : null,
-        React.createElement(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => {
-                model.setTrackName(event.target.value);
-            }, slotProps: {
-                htmlInput: { 'data-testid': 'trackNameInput' },
-            } }),
-        React.createElement(TrackAdapterSelector, { model: model }),
-        React.createElement(TrackTypeSelector, { model: model }),
-        React.createElement(AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => {
+    else {
+        const supportedForIndexing = isSupportedIndexingAdapter(trackAdapter.type);
+        const { pluginManager } = getEnv(model);
+        const Component = pluginManager.evaluateExtensionPoint('Core-addTrackComponent', ({ model }) => (_jsx(AssemblySelector, { session: session, helperText: "Select assembly to add track to", selected: model.assembly, onChange: asm => {
                 model.setAssembly(asm);
             }, TextFieldProps: {
                 fullWidth: true,
                 SelectProps: {
-                    // @ts-expect-error
-                    SelectDisplayProps: { 'data-testid': 'assemblyNameSelect' },
+                    SelectDisplayProps: {
+                        'data-testid': 'assemblyNameSelect',
+                    },
                 },
-            } }),
-        isElectron && supportedForIndexing && (React.createElement(FormControl, null,
-            React.createElement(FormControlLabel, { label: 'Index track for text searching?', control: React.createElement(Checkbox, { checked: check, onChange: e => {
-                        setCheck(e.target.checked);
-                        model.setTextIndexTrack(e.target.checked);
-                    } }) }))),
-        isElectron && check && supportedForIndexing ? (React.createElement(TextIndexingConfig, { model: model })) : null));
+            } })), { model });
+        return (_jsxs("div", { children: [_jsx(StatusMessage, { trackAdapter: trackAdapter, trackType: trackType }), warningMessage ? (_jsx(Typography, { color: "warning", children: warningMessage })) : null, _jsx(TextField, { className: classes.spacing, label: "trackName", helperText: "A name for this track", fullWidth: true, value: trackName, onChange: event => {
+                        model.setTrackName(event.target.value);
+                    }, slotProps: {
+                        htmlInput: {
+                            'data-testid': 'trackNameInput',
+                        },
+                    } }), _jsxs("div", { style: {
+                        display: 'flex',
+                        flexDirection: 'column',
+                        gap: 10,
+                    }, children: [_jsx(TrackAdapterSelector, { model: model }), _jsx(TrackTypeSelector, { model: model }), _jsx(Suspense, { fallback: null, children: _jsx(Component, { model: model }) })] }), isElectron && supportedForIndexing && (_jsx(FormControl, { children: _jsx(FormControlLabel, { label: "Index track for text searching?", control: _jsx(Checkbox, { checked: check, onChange: e => {
+                                setCheck(e.target.checked);
+                                model.setTextIndexTrack(e.target.checked);
+                            } }) }) })), isElectron && check && supportedForIndexing ? (_jsx(TextIndexingConfig, { model: model })) : null] }));
+    }
 });
 export default ConfirmTrack;

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

@@ -1,6 +1,5 @@
-import React from 'react';
-import { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model';
 declare const DefaultAddTrackWorkflow: ({ model, }: {
     model: AddTrackModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default DefaultAddTrackWorkflow;