@jbrowse/plugin-data-management 2.17.0 → 2.18.0

package/esm/HierarchicalTrackSelectorWidget/util.d.ts

@@ -1,5 +1,5 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { AbstractSessionModel } from '@jbrowse/core/util';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
 export declare function hasAnyOverlap<T>(a1?: T[], a2?: T[]): boolean;
 export declare function hasAllOverlap<T>(a1?: T[], a2?: T[]): boolean;
 export declare function matches(query: string, conf: AnyConfigurationModel, session: AbstractSessionModel): boolean;

package/esm/HierarchicalTrackSelectorWidget/util.js

@@ -1,8 +1,6 @@
-import { readConfObject, } from '@jbrowse/core/configuration';
+import { readConfObject } from '@jbrowse/core/configuration';
 import { getTrackName } from '@jbrowse/core/util/tracks';
 export function hasAnyOverlap(a1 = [], a2 = []) {
-    // shortcut case is that arrays are single entries, and are equal
-    // long case is that we use a set
     if (a1[0] === a2[0]) {
         return true;
     }
@@ -26,7 +24,6 @@ export function findSubCategories(obj, paths, depth = 0) {
     for (const elt of obj) {
         if (elt.children.length) {
             const hasSubCategories = findSubCategories(elt.children, paths, depth + 1);
-            // avoid pushing the root "Tracks" node by checking depth>0
             if (hasSubCategories && depth > 0) {
                 paths.push(elt.id);
             }

package/esm/PluginStoreWidget/components/AddCustomPluginDialog.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { PluginStoreModel } from '../model';
+import type { PluginStoreModel } from '../model';
 declare const AddCustomPluginDialog: ({ onClose, model, }: {
     onClose: () => void;
     model: PluginStoreModel;

package/esm/PluginStoreWidget/components/AddCustomPluginDialog.js

@@ -1,12 +1,11 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
 import { Dialog } from '@jbrowse/core/ui';
-import { Button, Collapse, DialogActions, DialogContent, DialogContentText, TextField, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
 import { getSession } from '@jbrowse/core/util';
-// icons
-import IconButton from '@mui/material/IconButton';
 import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
+import { Button, Collapse, DialogActions, DialogContent, DialogContentText, TextField, } from '@mui/material';
+import IconButton from '@mui/material/IconButton';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()(theme => ({
     dialogContent: {
         display: 'flex',

package/esm/PluginStoreWidget/components/DeletePluginDialog.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 import { Dialog } from '@jbrowse/core/ui';
+import { Button, DialogActions, DialogContent, Typography } from '@mui/material';
 export default function DeletePluginDialog({ onClose, plugin, }) {
     return (React.createElement(Dialog, { open: true, onClose: () => {
             onClose();
@@ -13,7 +13,6 @@ export default function DeletePluginDialog({ onClose, plugin, }) {
             React.createElement(Typography, { color: "error" }, "Note: if any resources in this session still use this plugin, it may cause your session to crash")),
         React.createElement(DialogActions, null,
             React.createElement(Button, { variant: "contained", color: "primary", onClick: () => {
-                    // avoid showing runtime plugin warning
                     window.setTimeout(() => {
                         onClose(plugin);
                     }, 500);

package/esm/PluginStoreWidget/components/InstalledPlugin.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { BasePlugin } from '@jbrowse/core/util/types';
-import { PluginStoreModel } from '../model';
+import type { PluginStoreModel } from '../model';
+import type { BasePlugin } from '@jbrowse/core/util/types';
 declare const InstalledPlugin: ({ plugin, model, }: {
     plugin: BasePlugin;
     model: PluginStoreModel;

package/esm/PluginStoreWidget/components/InstalledPlugin.js

@@ -1,12 +1,11 @@
-import React, { Suspense, lazy, useState } from 'react';
-import { observer } from 'mobx-react';
-import { IconButton, ListItem, Tooltip, Typography } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
+import React, { lazy } from 'react';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import { isSessionWithSessionPlugins } from '@jbrowse/core/util/types';
 import CloseIcon from '@mui/icons-material/Close';
 import LockIcon from '@mui/icons-material/Lock';
-import { getEnv, getSession } from '@jbrowse/core/util';
-import { isSessionWithSessionPlugins, } from '@jbrowse/core/util/types';
-// lazies
+import { IconButton, ListItem, Tooltip, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 const DeletePluginDialog = lazy(() => import('./DeletePluginDialog'));
 const useStyles = makeStyles()(() => ({
     lockedPluginTooltip: {
@@ -19,32 +18,34 @@ function LockedPlugin() {
         React.createElement(LockIcon, null)));
 }
 const InstalledPlugin = observer(function ({ plugin, model, }) {
-    const [dialogPlugin, setDialogPlugin] = useState();
     const { pluginManager } = getEnv(model);
     const session = getSession(model);
     const { jbrowse, adminMode } = session;
     const isSessionPlugin = isSessionWithSessionPlugins(session)
         ? session.sessionPlugins.some(p => { var _a; return ((_a = pluginManager.pluginMetadata[plugin.name]) === null || _a === void 0 ? void 0 : _a.url) === p.url; })
         : false;
-    return (React.createElement(React.Fragment, null,
-        dialogPlugin ? (React.createElement(Suspense, { fallback: null },
-            React.createElement(DeletePluginDialog, { plugin: dialogPlugin, onClose: name => {
-                    if (name) {
-                        const pluginMetadata = pluginManager.pluginMetadata[plugin.name];
-                        if (adminMode) {
-                            jbrowse.removePlugin(pluginMetadata);
-                        }
-                        else if (isSessionWithSessionPlugins(session)) {
-                            session.removeSessionPlugin(pluginMetadata);
-                        }
-                    }
-                    setDialogPlugin(undefined);
-                } }))) : null,
-        React.createElement(ListItem, { key: plugin.name },
-            adminMode || isSessionPlugin ? (React.createElement(IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => {
-                    setDialogPlugin(plugin.name);
-                } },
-                React.createElement(CloseIcon, null))) : (React.createElement(LockedPlugin, null)),
-            React.createElement(Typography, null, plugin.name))));
+    return (React.createElement(ListItem, { key: plugin.name },
+        adminMode || isSessionPlugin ? (React.createElement(IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => {
+                session.queueDialog(onClose => [
+                    DeletePluginDialog,
+                    {
+                        plugin: plugin.name,
+                        onClose: (name) => {
+                            if (name) {
+                                const pluginMetadata = pluginManager.pluginMetadata[plugin.name];
+                                if (adminMode) {
+                                    jbrowse.removePlugin(pluginMetadata);
+                                }
+                                else if (isSessionWithSessionPlugins(session)) {
+                                    session.removeSessionPlugin(pluginMetadata);
+                                }
+                            }
+                            onClose();
+                        },
+                    },
+                ]);
+            } },
+            React.createElement(CloseIcon, null))) : (React.createElement(LockedPlugin, null)),
+        React.createElement(Typography, null, plugin.name)));
 });
 export default InstalledPlugin;

package/esm/PluginStoreWidget/components/InstalledPluginsList.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { PluginStoreModel } from '../model';
+import type { PluginStoreModel } from '../model';
+import type PluginManager from '@jbrowse/core/PluginManager';
 declare const InstalledPluginsList: ({ pluginManager, model, }: {
     pluginManager: PluginManager;
     model: PluginStoreModel;

package/esm/PluginStoreWidget/components/InstalledPluginsList.js

@@ -1,6 +1,6 @@
 import React from 'react';
-import { observer } from 'mobx-react';
 import { List, Typography } from '@mui/material';
+import { observer } from 'mobx-react';
 import InstalledPlugin from './InstalledPlugin';
 const InstalledPluginsList = observer(function InstalledPluginsList({ pluginManager, model, }) {
     const { plugins } = pluginManager;

package/esm/PluginStoreWidget/components/PluginCard.d.ts

@@ -1,9 +1,8 @@
 import React from 'react';
-import { JBrowsePlugin } from '@jbrowse/core/util/types';
-import { PluginStoreModel } from '../model';
-declare const PluginCard: ({ plugin, model, adminMode, }: {
+import type { PluginStoreModel } from '../model';
+import type { JBrowsePlugin } from '@jbrowse/core/util/types';
+declare const PluginCard: ({ plugin, model, }: {
     plugin: JBrowsePlugin;
     model: PluginStoreModel;
-    adminMode: boolean;
 }) => React.JSX.Element;
 export default PluginCard;

package/esm/PluginStoreWidget/components/PluginCard.js

@@ -1,14 +1,12 @@
 import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { getParent } from 'mobx-state-tree';
-import { getSession, getEnv } from '@jbrowse/core/util';
-import { isSessionWithSessionPlugins, } from '@jbrowse/core/util/types';
-import { Card, CardActions, CardContent, Button, Link, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-// icons
-import PersonIcon from '@mui/icons-material/Person';
+import { getEnv, getSession } from '@jbrowse/core/util';
+import { isSessionWithSessionPlugins } from '@jbrowse/core/util/types';
 import AddIcon from '@mui/icons-material/Add';
 import CheckIcon from '@mui/icons-material/Check';
+import PersonIcon from '@mui/icons-material/Person';
+import { Button, Card, CardActions, CardContent, Link, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
 const useStyles = makeStyles()({
     card: {
         margin: '0.5em',
@@ -24,35 +22,39 @@ const useStyles = makeStyles()({
         display: 'flex',
         alignItems: 'center',
     },
+    mr: {
+        marginRight: '0.5em',
+    },
 });
-const PluginCard = observer(function PluginCard({ plugin, model, adminMode, }) {
+const PluginCard = observer(function PluginCard({ plugin, model, }) {
     const { classes } = useStyles();
     const session = getSession(model);
     const { pluginManager } = getEnv(model);
     const { runtimePluginDefinitions } = pluginManager;
-    // @ts-expect-error
-    const isInstalled = runtimePluginDefinitions.some(d => d.url === plugin.url);
+    const isInstalled = runtimePluginDefinitions.some(d => 'url' in d && d.url === plugin.url);
     const [tempDisabled, setTempDisabled] = useState(false);
-    const disableButton = isInstalled || tempDisabled;
-    const rootModel = getParent(model, 3);
-    const { jbrowse } = rootModel;
-    return (React.createElement(Card, { variant: "outlined", key: plugin.name, className: classes.card },
+    const { adminMode, jbrowse } = session;
+    const { name, authors, description } = plugin;
+    return (React.createElement(Card, { variant: "outlined", key: name, className: classes.card },
         React.createElement(CardContent, null,
             React.createElement(Typography, { variant: "h5" },
                 React.createElement(Link, { href: `${plugin.location}#readme`, target: "_blank", rel: "noopener" }, plugin.name)),
             React.createElement("div", { className: classes.dataField },
-                React.createElement(PersonIcon, { style: { marginRight: '0.5em' } }),
-                React.createElement(Typography, null, plugin.authors.join(', '))),
+                React.createElement(PersonIcon, { className: classes.mr }),
+                React.createElement(Typography, null, authors.join(', '))),
             React.createElement(Typography, { className: classes.bold }, "Description:"),
-            React.createElement(Typography, null, plugin.description)),
+            React.createElement(Typography, null, description)),
         React.createElement(CardActions, null,
-            React.createElement(Button, { variant: "contained", disabled: disableButton, startIcon: isInstalled ? React.createElement(CheckIcon, null) : React.createElement(AddIcon, null), onClick: () => {
+            React.createElement(Button, { variant: "contained", disabled: isInstalled || tempDisabled, startIcon: isInstalled ? React.createElement(CheckIcon, null) : React.createElement(AddIcon, null), onClick: () => {
                     if (adminMode) {
-                        jbrowse.addPlugin({ name: plugin.name, url: plugin.url });
+                        jbrowse.addPlugin(plugin);
                     }
                     else if (isSessionWithSessionPlugins(session)) {
                         session.addSessionPlugin(plugin);
                     }
+                    else {
+                        session.notify('No way to install plugin');
+                    }
                     setTempDisabled(true);
                 } }, isInstalled ? 'Installed' : 'Install'))));
 });

package/esm/PluginStoreWidget/components/PluginStoreWidget.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { PluginStoreModel } from '../model';
+import type { PluginStoreModel } from '../model';
 declare const PluginStoreWidget: ({ model, }: {
     model: PluginStoreModel;
 }) => React.JSX.Element;

package/esm/PluginStoreWidget/components/PluginStoreWidget.js

@@ -1,19 +1,16 @@
-import React, { useState, lazy, Suspense } from 'react';
-import { Accordion, AccordionSummary, Button, IconButton, InputAdornment, TextField, Typography, } from '@mui/material';
-import { makeStyles } from 'tss-react/mui';
-import { observer } from 'mobx-react';
-import { getEnv } from 'mobx-state-tree';
+import React, { lazy } from 'react';
 import { LoadingEllipses } from '@jbrowse/core/ui';
 import { getSession, isElectron } from '@jbrowse/core/util';
-// icons
-import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import ClearIcon from '@mui/icons-material/Clear';
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore';
 import InfoOutlinedIcon from '@mui/icons-material/InfoOutlined';
-// locals
+import { Accordion, AccordionSummary, Button, IconButton, InputAdornment, TextField, Typography, } from '@mui/material';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
 import InstalledPluginsList from './InstalledPluginsList';
 import PluginCard from './PluginCard';
 import { useFetchPlugins } from './util';
-// lazies
 const AddCustomPluginDialog = lazy(() => import('./AddCustomPluginDialog'));
 const useStyles = makeStyles()(theme => ({
     expandIcon: {
@@ -30,28 +27,36 @@ const useStyles = makeStyles()(theme => ({
         margin: '1em auto',
         display: 'flex',
     },
+    mr: {
+        marginRight: '0.3em',
+    },
+    m: {
+        margin: '1em',
+    },
 }));
 const PluginStoreWidget = observer(function ({ model, }) {
     const { classes } = useStyles();
     const { plugins, error } = useFetchPlugins();
-    const [open, setOpen] = useState(false);
-    const { adminMode } = getSession(model);
+    const session = getSession(model);
+    const { adminMode } = session;
     const { pluginManager } = getEnv(model);
     return (React.createElement("div", null,
         adminMode && (React.createElement(React.Fragment, null,
             !isElectron && (React.createElement("div", { className: classes.adminBadge },
-                React.createElement(InfoOutlinedIcon, { style: { marginRight: '0.3em' } }),
+                React.createElement(InfoOutlinedIcon, { className: classes.mr }),
                 React.createElement(Typography, null,
                     "You are using the ",
                     React.createElement("code", null, "admin-server"),
                     ". Any changes you make will be saved to your configuration file. You also have the ability to add custom plugins that are not in the store."))),
             React.createElement(Button, { className: classes.customPluginButton, variant: "contained", onClick: () => {
-                    setOpen(true);
-                } }, "Add custom plugin"),
-            open ? (React.createElement(Suspense, { fallback: null },
-                React.createElement(AddCustomPluginDialog, { onClose: () => {
-                        setOpen(false);
-                    }, model: model }))) : null)),
+                    session.queueDialog(onClose => [
+                        AddCustomPluginDialog,
+                        {
+                            model,
+                            onClose,
+                        },
+                    ]);
+                } }, "Add custom plugin"))),
         React.createElement(TextField, { label: "Filter plugins", value: model.filterText, onChange: event => {
                 model.setFilterText(event.target.value);
             }, fullWidth: true, slotProps: {
@@ -66,19 +71,18 @@ const PluginStoreWidget = observer(function ({ model, }) {
         React.createElement(Accordion, { defaultExpanded: true },
             React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
                 React.createElement(Typography, { variant: "h5" }, "Installed plugins")),
-            React.createElement("div", { style: { margin: '1em' } },
+            React.createElement("div", { className: classes.m },
                 React.createElement(InstalledPluginsList, { pluginManager: pluginManager, model: model }))),
         React.createElement(Accordion, { defaultExpanded: true },
             React.createElement(AccordionSummary, { expandIcon: React.createElement(ExpandMoreIcon, { className: classes.expandIcon }) },
                 React.createElement(Typography, { variant: "h5" }, "Available plugins")),
             error ? (React.createElement(Typography, { color: "error" }, `${error}`)) : plugins ? (plugins
                 .filter(plugin => {
-                // If plugin only has cjsUrl, don't display outside desktop
                 return (!(isElectron && plugin.cjsUrl) &&
                     plugin.name
                         .toLowerCase()
                         .includes(model.filterText.toLowerCase()));
             })
-                .map(plugin => (React.createElement(PluginCard, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (React.createElement(LoadingEllipses, null)))));
+                .map(plugin => (React.createElement(PluginCard, { key: plugin.name, plugin: plugin, model: model })))) : (React.createElement(LoadingEllipses, null)))));
 });
 export default PluginStoreWidget;

package/esm/PluginStoreWidget/components/util.d.ts

@@ -1,4 +1,4 @@
-import { JBrowsePlugin } from '@jbrowse/core/util/types';
+import type { JBrowsePlugin } from '@jbrowse/core/util/types';
 export declare function useFetchPlugins(): {
     plugins: JBrowsePlugin[] | undefined;
     error: unknown;

package/esm/PluginStoreWidget/components/util.js

@@ -1,9 +1,8 @@
-import { useState, useEffect } from 'react';
+import { useEffect, useState } from 'react';
 export function useFetchPlugins() {
     const [plugins, setPlugins] = useState();
     const [error, setError] = useState();
     useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {

package/esm/PluginStoreWidget/index.d.ts

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

package/esm/PluginStoreWidget/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 stateModelFactory from './model';
 const configSchema = ConfigurationSchema('PluginStoreWidget', {});
 export default function PluginStoreWidgetF(pluginManager) {

package/esm/PluginStoreWidget/model.d.ts

@@ -1,18 +1,12 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export default function stateModelFactory(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<"PluginStoreWidget">;
     filterText: import("mobx-state-tree").IType<string | undefined, string, string>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
-    /**
-     * #action
-     */
     clearFilterText(): void;
-    /**
-     * #action
-     */
     setFilterText(newText: string): void;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type PluginStoreStateModel = ReturnType<typeof stateModelFactory>;

package/esm/PluginStoreWidget/model.js

@@ -1,35 +1,17 @@
-import { types } from 'mobx-state-tree';
 import { ElementId } from '@jbrowse/core/util/types/mst';
+import { types } from 'mobx-state-tree';
 export default function stateModelFactory(pluginManager) {
     return types
         .model('PluginStoreModel', {
-        /**
-         * #property
-         */
         id: ElementId,
-        /**
-         * #property
-         */
         type: types.literal('PluginStoreWidget'),
-        /**
-         * #property
-         */
         filterText: '',
-        /**
-         * #property
-         */
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         clearFilterText() {
             self.filterText = '';
         },
-        /**
-         * #action
-         */
         setFilterText(newText) {
             self.filterText = newText;
         },

package/esm/{ucsc-trackhub → UCSCTrackHub}/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     hubTxtLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +7,6 @@ declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/config
         };
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: string;
         defaultValue: never[];

package/esm/{ucsc-trackhub → UCSCTrackHub}/configSchema.js

@@ -1,13 +1,7 @@
-import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config UCSCTrackHubConnection
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
+function x() { }
 const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
-    /**
-     * #slot
-     */
     hubTxtLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,18 +10,12 @@ const UCSCTrackHubConnection = ConfigurationSchema('UCSCTrackHubConnection', {
         },
         description: 'location of the hub file (usually called hub.txt)',
     },
-    /**
-     * #slot
-     */
     assemblyNames: {
         type: 'stringArray',
         defaultValue: [],
         description: 'optional list of genomes to import from this track hub, if empty all genomes will be imported',
     },
 }, {
-    /**
-     * #baseConfiguration
-     */
     baseConfiguration: baseConnectionConfig,
 });
 export default UCSCTrackHubConnection;

package/{dist/ucsc-trackhub → esm/UCSCTrackHub}/doConnect.d.ts

@@ -1,4 +1,4 @@
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 export declare function doConnect(self: {
     configuration: AnyConfigurationModel;
     addTrackConfs: (arg: Record<string, unknown>[]) => void;

package/esm/{ucsc-trackhub → UCSCTrackHub}/doConnect.js

@@ -1,9 +1,9 @@
 import { HubFile, SingleFileHub } from '@gmod/ucsc-hub';
-import { generateTracks, fetchGenomesFile, fetchTrackDbFile, } from './ucscTrackHub';
 import { getConf } from '@jbrowse/core/configuration';
 import { getSession } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { nanoid } from '@jbrowse/core/util/nanoid';
+import { fetchGenomesFile, fetchTrackDbFile, generateTracks, } from './ucscTrackHub';
 function resolve(uri, baseUri) {
     return new URL(uri, baseUri).href;
 }
@@ -14,7 +14,6 @@ export async function doConnect(self) {
     try {
         const hubFileLocation = getConf(self, 'hubTxtLocation');
         const hubFileText = await openLocation(hubFileLocation).readFile('utf8');
-        // @ts-expect-error
         const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
         const { assemblyManager } = session;
         if (hubFileText.includes('useOneFile on')) {
@@ -23,7 +22,6 @@ export async function doConnect(self) {
             const genomeName = genome.name;
             const asm = assemblyManager.get(genomeName);
             if (!asm) {
-                // @ts-expect-error
                 session.addSessionAssembly({
                     name: genomeName,
                     sequence: {
@@ -57,7 +55,6 @@ export async function doConnect(self) {
             if (!genomeFile) {
                 throw new Error('genomesFile not found on hub');
             }
-            // @ts-expect-error
             const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
             const genomesFileLocation = hubUri
                 ? {
@@ -80,7 +77,6 @@ export async function doConnect(self) {
                     notLoadedAssemblies.push(genomeName);
                     continue;
                 }
-                // @ts-expect-error
                 const db = genome.data.trackDb;
                 if (!db) {
                     throw new Error('genomesFile not found on hub');

package/esm/{ucsc-trackhub → UCSCTrackHub}/index.d.ts

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

package/esm/UCSCTrackHub/index.js

@@ -0,0 +1,15 @@
+import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
+import configSchema from './configSchema';
+import stateModelFactory from './model';
+export default function UCSCTrackHubConnectionF(pluginManager) {
+    pluginManager.addConnectionType(() => {
+        return new ConnectionType({
+            name: 'UCSCTrackHubConnection',
+            configSchema,
+            stateModel: stateModelFactory(pluginManager),
+            displayName: 'UCSC Track Hub',
+            description: 'A track or assembly hub in the Track Hub format',
+            url: 'https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
+        });
+    });
+}

package/esm/{ucsc-trackhub → UCSCTrackHub}/model.d.ts

@@ -1,8 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-/**
- * #stateModel UCSCTrackHubConnection
- * extends BaseConnectionModel
- */
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
@@ -19,9 +15,6 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
-    /**
-     * #property
-     */
     configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         hubTxtLocation: {
             type: string;
@@ -48,9 +41,6 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             description: string;
         };
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
 }, {
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
@@ -81,8 +71,5 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
     setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
-    /**
-     * #action
-     */
     connect(): Promise<void>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;