@jbrowse/plugin-data-management 3.6.5 → 4.0.0

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

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

package/esm/AddConnectionWidget/components/AddConnectionWidget.js

@@ -1,12 +1,12 @@
 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 { makeStyles } from '@jbrowse/core/util/tss-react';
 import { isSessionWithConnections } from '@jbrowse/product-core';
 import { Button, Step, StepContent, StepLabel, Stepper } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import ConfigureConnection from './ConfigureConnection';
-import ConnectionTypeSelect from './ConnectionTypeSelect';
+import ConfigureConnection from "./ConfigureConnection.js";
+import ConnectionTypeSelect from "./ConnectionTypeSelect.js";
 const useStyles = makeStyles()(theme => ({
     root: {
         marginTop: theme.spacing(1),
@@ -23,14 +23,14 @@ const useStyles = makeStyles()(theme => ({
     },
 }));
 const steps = ['Select a Connection Type', 'Configure Connection'];
-const AddConnectionWidget = observer(function ({ model }) {
+const AddConnectionWidget = observer(function AddConnectionWidget({ model, }) {
     const [connectionType, setConnectionType] = useState();
     const [connectionId, setConnectionId] = useState();
     const [activeStep, setActiveStep] = useState(0);
     const { classes } = useStyles();
     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]);
+    const configModel = useMemo(() => connectionType?.configSchema.create({ connectionId }, getEnv(model)), [connectionId, connectionType, model]);
     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) {

package/esm/AddConnectionWidget/components/ConfigureConnection.js

@@ -3,7 +3,7 @@ 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 ConfigureConnection = observer(function ConfigureConnection({ connectionType, model, session, }) {
     const ConfigEditorComponent = connectionType.configEditorComponent || ConfigurationEditor;
     return (_jsx(Suspense, { fallback: _jsx(LoadingEllipses, {}), children: _jsx(ConfigEditorComponent, { model: { target: model }, session: session }) }));
 });

package/esm/AddConnectionWidget/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import stateModel from './model';
+import stateModel from "./model.js";
 const configSchema = ConfigurationSchema('AddConnectionWidget', {});
 export default function AddConnectionWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
@@ -10,7 +10,7 @@ export default function AddConnectionWidgetF(pluginManager) {
             heading: 'Add a connection',
             configSchema,
             stateModel,
-            ReactComponent: lazy(() => import('./components/AddConnectionWidget')),
+            ReactComponent: lazy(() => import("./components/AddConnectionWidget.js")),
         });
     });
 }

package/esm/AddConnectionWidget/model.d.ts

@@ -1,5 +1,5 @@
-declare const _default: import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AddConnectionWidget">;
-}, {}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+declare const _default: import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"AddConnectionWidget">;
+}, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export default _default;

package/esm/AddConnectionWidget/model.js

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

package/esm/AddTrackWidget/components/AddTrackStatusMessage.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
@@ -9,5 +9,5 @@ const useStyles = makeStyles()(theme => ({
 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."] }));
+    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?.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

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

package/esm/AddTrackWidget/components/AddTrackUnknownAdapterPrompt.js

@@ -1,8 +1,8 @@
 import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
 import { ExternalLink } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import TrackAdapterSelector from './TrackAdapterSelector';
+import TrackAdapterSelector from "./TrackAdapterSelector.js";
 const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const AddTrackSelector: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/AddTrackWidget.js

@@ -3,9 +3,9 @@ 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, }) {
+import DefaultAddTrackWorkflow from "./DefaultAddTrackWorkflow.js";
+import PasteConfigWorkflow from "./PasteConfigWorkflow.js";
+const AddTrackSelector = observer(function AddTrackSelector({ model, }) {
     const [val, setVal] = useState('Default add track workflow');
     const ComponentMap = {
         'Default add track workflow': DefaultAddTrackWorkflow,

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const ConfirmTrack: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/ConfirmTrack.js

@@ -3,15 +3,15 @@ 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 { makeStyles } from '@jbrowse/core/util/tss-react';
 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 TrackAdapterSelector from './TrackAdapterSelector';
-import TrackTypeSelector from './TrackTypeSelector';
-import Unsupported from './Unsupported';
+import StatusMessage from "./AddTrackStatusMessage.js";
+import UnknownAdapterPrompt from "./AddTrackUnknownAdapterPrompt.js";
+import TextIndexingConfig from "./TextIndexingConfig.js";
+import TrackAdapterSelector from "./TrackAdapterSelector.js";
+import TrackTypeSelector from "./TrackTypeSelector.js";
+import Unsupported from "./Unsupported.js";
 const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),
@@ -26,14 +26,14 @@ const ConfirmTrack = observer(function ConfirmTrack({ model, }) {
         if (adapterHint === '' && trackAdapter) {
             model.setAdapterHint(trackAdapter.type);
         }
-    }, [adapterHint, trackAdapter, trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type, model]);
+    }, [adapterHint, trackAdapter, trackAdapter?.type, model]);
     if (unsupported) {
         return _jsx(Unsupported, {});
     }
-    else if ((trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) === UNKNOWN) {
+    else if (trackAdapter?.type === UNKNOWN) {
         return _jsx(UnknownAdapterPrompt, { model: model });
     }
-    else if (!(trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type)) {
+    else if (!trackAdapter?.type) {
         return _jsx(Typography, { children: "Could not recognize this data type." });
     }
     else {

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const DefaultAddTrackWorkflow: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/DefaultAddTrackWorkflow.js

@@ -1,12 +1,12 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { getSession } from '@jbrowse/core/util';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Button, Step, StepContent, StepLabel, Stepper, Typography, } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import ConfirmTrack from './ConfirmTrack';
-import TrackSourceSelect from './TrackSourceSelect';
-import { doSubmit } from './doSubmit';
+import ConfirmTrack from "./ConfirmTrack.js";
+import TrackSourceSelect from "./TrackSourceSelect.js";
+import { doSubmit } from "./doSubmit.js";
 const useStyles = makeStyles()(theme => ({
     root: {
         marginTop: theme.spacing(1),
@@ -21,12 +21,9 @@ const useStyles = makeStyles()(theme => ({
         marginTop: theme.spacing(10),
         marginBottom: theme.spacing(2),
     },
-    alertContainer: {
-        padding: `${theme.spacing(2)}px 0px ${theme.spacing(2)}px 0px`,
-    },
 }));
 const steps = ['Enter track data', 'Confirm track type'];
-const DefaultAddTrackWorkflow = observer(function ({ model, }) {
+const DefaultAddTrackWorkflow = observer(function DefaultAddTrackWorkflow({ model, }) {
     const [activeStep, setActiveStep] = useState(0);
     const { classes } = useStyles();
     const { assembly, trackAdapter, trackData, trackName, trackType } = model;
@@ -45,7 +42,7 @@ const DefaultAddTrackWorkflow = observer(function ({ model, }) {
             case 0:
                 return !trackData;
             case 1:
-                return !(trackName && trackType && (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) && assembly);
+                return !(trackName && trackType && trackAdapter?.type && assembly);
             default:
                 return true;
         }

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

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

package/esm/AddTrackWidget/components/PasteConfigWorkflow.js

@@ -2,10 +2,10 @@ import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
 import { getSession, isSessionModelWithWidgets, isSessionWithAddTracks, } from '@jbrowse/core/util';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Button, TextField } from '@mui/material';
 import { transaction } from 'mobx';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     textbox: {
         width: '100%',
@@ -16,7 +16,7 @@ const useStyles = makeStyles()({
         display: 'block',
     },
 });
-const PasteConfigAddTrackWorkflow = observer(function ({ model, }) {
+const PasteConfigAddTrackWorkflow = observer(function PasteConfigAddTrackWorkflow({ model }) {
     const { classes } = useStyles();
     const [val, setVal] = useState('');
     const [error, setError] = useState();

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const TextIndexingConfig: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/TextIndexingConfig.js

@@ -1,10 +1,10 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { useEffect, useState } from 'react';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import AddIcon from '@mui/icons-material/Add';
 import DeleteIcon from '@mui/icons-material/Delete';
 import { Card, CardContent, IconButton, InputAdornment, InputLabel, List, ListItem, Paper, TextField, } from '@mui/material';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     paper: {
         display: 'flex',
@@ -15,7 +15,7 @@ const useStyles = makeStyles()(theme => ({
         marginTop: theme.spacing(1),
     },
 }));
-const TextIndexingConfig = observer(function ({ model, }) {
+const TextIndexingConfig = observer(function TextIndexingConfig({ model, }) {
     const { classes } = useStyles();
     const [value1, setValue1] = useState('');
     const [value2, setValue2] = useState('');

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

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

package/esm/AddTrackWidget/components/TrackAdapterSelector.js

@@ -2,11 +2,11 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { getEnv } from '@jbrowse/core/util';
 import { ListSubheader, MenuItem, TextField } from '@mui/material';
 import { observer } from 'mobx-react';
-import { categorizeAdapters } from './util';
-const TrackAdapterSelector = observer(({ model }) => {
+import { categorizeAdapters } from "./util.js";
+const TrackAdapterSelector = observer(function ({ model, }) {
     const { trackAdapter } = model;
     const { pluginManager } = getEnv(model);
-    return (_jsx(TextField, { value: (trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type) !== 'UNKNOWN' ? trackAdapter === null || trackAdapter === void 0 ? void 0 : trackAdapter.type : '', label: "Adapter type", variant: "outlined", select: true, fullWidth: true, onChange: event => {
+    return (_jsx(TextField, { value: trackAdapter?.type !== 'UNKNOWN' ? trackAdapter?.type : '', label: "Adapter type", variant: "outlined", select: true, fullWidth: true, onChange: event => {
             model.setAdapterHint(event.target.value);
         }, slotProps: {
             select: {
@@ -16,7 +16,7 @@ const TrackAdapterSelector = observer(({ model }) => {
             },
         }, children: Object.entries(categorizeAdapters(pluginManager
             .getAdapterElements()
-            .filter(e => { var _a; return !((_a = e.adapterMetadata) === null || _a === void 0 ? void 0 : _a.hiddenFromGUI); }))).map(([key, val]) => [
+            .filter(e => !e.adapterMetadata?.hiddenFromGUI))).map(([key, val]) => [
             _jsx(ListSubheader, { children: key }, key),
             val.map(elt => (_jsx(MenuItem, { value: elt.name, children: elt.displayName }, elt.name))),
         ]) }));

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const TrackSourceSelect: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/TrackSourceSelect.js

@@ -1,9 +1,9 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { FileSelector } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
+import { getRoot } from '@jbrowse/mobx-state-tree';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import { getRoot } from 'mobx-state-tree';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     paper: {
         padding: theme.spacing(2),
@@ -12,7 +12,7 @@ const useStyles = makeStyles()(theme => ({
         height: theme.spacing(8),
     },
 }));
-const TrackSourceSelect = observer(function ({ model, }) {
+const TrackSourceSelect = observer(function TrackSourceSelect({ model, }) {
     const { classes } = useStyles();
     const rootModel = getRoot(model);
     return (_jsxs(Paper, { className: classes.paper, children: [_jsx(FileSelector, { name: "Main file", description: "", location: model.trackData, setLocation: model.setTrackData, setName: model.setTrackName, rootModel: rootModel }), _jsx("div", { className: classes.spacer }), _jsx(FileSelector, { name: "Index file", description: "(Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.", location: model.indexTrackData, setLocation: model.setIndexTrackData, setName: model.setTrackName, rootModel: rootModel })] }));

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 declare const TrackTypeSelector: ({ model, }: {
     model: AddTrackModel;
 }) => import("react/jsx-runtime").JSX.Element;

package/esm/AddTrackWidget/components/TrackTypeSelector.js

@@ -2,7 +2,7 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import { getEnv } from '@jbrowse/core/util';
 import { MenuItem, TextField } from '@mui/material';
 import { observer } from 'mobx-react';
-const TrackTypeSelector = observer(function ({ model, }) {
+const TrackTypeSelector = observer(function TrackTypeSelector({ model, }) {
     const { pluginManager } = getEnv(model);
     const { trackType } = model;
     const trackTypes = pluginManager.getTrackElements();

package/esm/AddTrackWidget/components/Unsupported.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { ExternalLink } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { Typography } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     spacing: {
         marginBottom: theme.spacing(3),

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

@@ -1,4 +1,4 @@
-import type { AddTrackModel } from '../model';
+import type { AddTrackModel } from '../model.ts';
 export declare function doSubmit({ model }: {
     model: AddTrackModel;
 }): void;

package/esm/AddTrackWidget/components/doSubmit.js

@@ -1,5 +1,5 @@
 import { getSession, isElectron, isSessionModelWithWidgets, isSessionWithAddTracks, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
-import { getRoot } from 'mobx-state-tree';
+import { getRoot } from '@jbrowse/mobx-state-tree';
 function doTextIndexTrack({ trackId, model, }) {
     const { textIndexingConf, trackName, assembly } = model;
     const { jobsManager } = getRoot(model);
@@ -22,7 +22,6 @@ function doTextIndexTrack({ trackId, model, }) {
     });
 }
 export function doSubmit({ model }) {
-    var _a;
     const { textIndexTrack, trackAdapter, view } = model;
     const session = getSession(model);
     const trackConfig = model.getTrackConfig(Date.now());
@@ -32,7 +31,7 @@ export function doSubmit({ model }) {
     else if (trackConfig && trackAdapter) {
         const { trackId } = trackConfig;
         session.addTrackConf(trackConfig);
-        (_a = view === null || view === void 0 ? void 0 : view.showTrack) === null || _a === void 0 ? void 0 : _a.call(view, trackId);
+        view?.showTrack?.(trackId);
         if (isElectron &&
             textIndexTrack &&
             isSupportedIndexingAdapter(trackAdapter.type)) {

package/esm/AddTrackWidget/components/util.js

@@ -1,8 +1,7 @@
 export function categorizeAdapters(adaptersList) {
-    var _a;
     const map = {};
     for (const adapter of adaptersList) {
-        const key = ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) || 'Default';
+        const key = adapter.adapterMetadata?.category || 'Default';
         if (!map[key]) {
             map[key] = [];
         }

package/esm/AddTrackWidget/index.js

@@ -1,7 +1,7 @@
 import { lazy } from 'react';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { WidgetType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './model';
+import stateModelFactory from "./model.js";
 const configSchema = ConfigurationSchema('AddTrackWidget', {});
 export default function AddTrackWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
@@ -10,7 +10,7 @@ export default function AddTrackWidgetF(pluginManager) {
             heading: 'Add a track',
             configSchema,
             stateModel: stateModelFactory(pluginManager),
-            ReactComponent: lazy(() => import('./components/AddTrackWidget')),
+            ReactComponent: lazy(() => import("./components/AddTrackWidget.js")),
         });
     });
 }

package/esm/AddTrackWidget/model.d.ts

@@ -1,14 +1,14 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { FileLocation } from '@jbrowse/core/util/types';
-import type { Instance } from 'mobx-state-tree';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 interface IndexingAttr {
     attributes: string[];
     exclude: string[];
 }
-export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
+export default function f(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    id: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"AddTrackWidget">;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
 }, {
     trackSource: string;
     trackData: FileLocation | undefined;
@@ -33,7 +33,7 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     setTrackType(str: string): void;
     clearData(): void;
 } & {
-    readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
+    readonly trackAdapter: import("@jbrowse/core/util").AdapterConfig | undefined;
     readonly trackName: string;
     readonly isFtp: boolean;
     readonly isRelativeTrackUrl: boolean;
@@ -52,13 +52,10 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
         type: string;
         name: string;
         assemblyNames: any[];
-        adapter: {
-            sequenceAdapter: any;
-            type: string;
-        };
+        adapter: import("@jbrowse/core/util").AdapterConfig;
     } | undefined;
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type AddTrackStateModel = ReturnType<typeof f>;
 export type AddTrackModel = Instance<AddTrackStateModel>;
 export {};

package/esm/AddTrackWidget/model.js

@@ -1,9 +1,8 @@
-import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { UNSUPPORTED, getFileName, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from '@jbrowse/mobx-state-tree';
 import deepmerge from 'deepmerge';
-import { types } from 'mobx-state-tree';
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);
@@ -88,46 +87,38 @@ export default function f(pluginManager) {
                 (self.trackData ? getFileName(self.trackData) : ''));
         },
         get isFtp() {
-            var _a, _b;
             const { trackData: track, indexTrackData: index } = self;
-            return !!((((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
+            return !!((index?.uri?.startsWith('ftp://') || track?.uri?.startsWith('ftp://')));
         },
         get isRelativeTrackUrl() {
-            var _a;
-            const uri = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri;
+            const uri = self.trackData?.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
         get isRelativeIndexUrl() {
-            var _a;
-            const uri = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri;
+            const uri = self.indexTrackData?.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
         get isRelativeUrl() {
             return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
         },
         get trackHttp() {
-            var _a, _b;
-            return (_b = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
+            return self.trackData?.uri?.startsWith('http://');
         },
         get indexHttp() {
-            var _a, _b;
-            return (_b = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
+            return self.indexTrackData?.uri?.startsWith('http://');
         },
         get wrongProtocol() {
             return (window.location.protocol === 'https:' &&
                 (this.trackHttp || this.indexHttp));
         },
         get unsupported() {
-            var _a;
-            return ((_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type) === UNSUPPORTED;
+            return this.trackAdapter?.type === UNSUPPORTED;
         },
         get assembly() {
-            var _a;
-            return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
+            return self.altAssemblyName || self.view.assemblyNames?.[0];
         },
         get trackAdapterType() {
-            var _a;
-            return (_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type;
+            return this.trackAdapter?.type;
         },
         get trackType() {
             return (self.altTrackType ||
@@ -151,13 +142,7 @@ export default function f(pluginManager) {
                     type: self.trackType,
                     name: self.trackName,
                     assemblyNames: [self.assembly],
-                    adapter: {
-                        ...self.trackAdapter,
-                        sequenceAdapter: getConf(assemblyInstance, [
-                            'sequence',
-                            'adapter',
-                        ]),
-                    },
+                    adapter: self.trackAdapter,
                 }, self.mixinData)
                 : undefined;
         },