@jbrowse/plugin-data-management 2.16.1 → 2.18.0

package/dist/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/dist/HierarchicalTrackSelectorWidget/util.js

@@ -8,8 +8,6 @@ exports.findTopLevelCategories = findTopLevelCategories;
 const configuration_1 = require("@jbrowse/core/configuration");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 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;
     }
@@ -33,7 +31,6 @@ 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/dist/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/dist/PluginStoreWidget/components/AddCustomPluginDialog.js

@@ -27,14 +27,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
 const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
-// icons
-const IconButton_1 = __importDefault(require("@mui/material/IconButton"));
 const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
+const material_1 = require("@mui/material");
+const IconButton_1 = __importDefault(require("@mui/material/IconButton"));
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     dialogContent: {
         display: 'flex',

package/dist/PluginStoreWidget/components/DeletePluginDialog.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = DeletePluginDialog;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
 const ui_1 = require("@jbrowse/core/ui");
+const material_1 = require("@mui/material");
 function DeletePluginDialog({ onClose, plugin, }) {
     return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: () => {
             onClose();
@@ -19,7 +19,6 @@ function DeletePluginDialog({ onClose, plugin, }) {
             react_1.default.createElement(material_1.Typography, { color: "error" }, "Note: if any resources in this session still use this plugin, it may cause your session to crash")),
         react_1.default.createElement(material_1.DialogActions, null,
             react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                    // avoid showing runtime plugin warning
                     window.setTimeout(() => {
                         onClose(plugin);
                     }, 500);

package/dist/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/dist/PluginStoreWidget/components/InstalledPlugin.js

@@ -27,14 +27,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const Close_1 = __importDefault(require("@mui/icons-material/Close"));
-const Lock_1 = __importDefault(require("@mui/icons-material/Lock"));
 const util_1 = require("@jbrowse/core/util");
 const types_1 = require("@jbrowse/core/util/types");
-// lazies
+const Close_1 = __importDefault(require("@mui/icons-material/Close"));
+const Lock_1 = __importDefault(require("@mui/icons-material/Lock"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const DeletePluginDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./DeletePluginDialog'))));
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     lockedPluginTooltip: {
@@ -47,32 +46,34 @@ function LockedPlugin() {
         react_1.default.createElement(Lock_1.default, null)));
 }
 const InstalledPlugin = (0, mobx_react_1.observer)(function ({ plugin, model, }) {
-    const [dialogPlugin, setDialogPlugin] = (0, react_1.useState)();
     const { pluginManager } = (0, util_1.getEnv)(model);
     const session = (0, util_1.getSession)(model);
     const { jbrowse, adminMode } = session;
     const isSessionPlugin = (0, types_1.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_1.default.createElement(react_1.default.Fragment, null,
-        dialogPlugin ? (react_1.default.createElement(react_1.Suspense, { fallback: null },
-            react_1.default.createElement(DeletePluginDialog, { plugin: dialogPlugin, onClose: name => {
-                    if (name) {
-                        const pluginMetadata = pluginManager.pluginMetadata[plugin.name];
-                        if (adminMode) {
-                            jbrowse.removePlugin(pluginMetadata);
-                        }
-                        else if ((0, types_1.isSessionWithSessionPlugins)(session)) {
-                            session.removeSessionPlugin(pluginMetadata);
-                        }
-                    }
-                    setDialogPlugin(undefined);
-                } }))) : null,
-        react_1.default.createElement(material_1.ListItem, { key: plugin.name },
-            adminMode || isSessionPlugin ? (react_1.default.createElement(material_1.IconButton, { "data-testid": `removePlugin-${plugin.name}`, onClick: () => {
-                    setDialogPlugin(plugin.name);
-                } },
-                react_1.default.createElement(Close_1.default, null))) : (react_1.default.createElement(LockedPlugin, null)),
-            react_1.default.createElement(material_1.Typography, null, plugin.name))));
+    return (react_1.default.createElement(material_1.ListItem, { key: plugin.name },
+        adminMode || isSessionPlugin ? (react_1.default.createElement(material_1.IconButton, { "data-testid": `removePlugin-${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 ((0, types_1.isSessionWithSessionPlugins)(session)) {
+                                    session.removeSessionPlugin(pluginMetadata);
+                                }
+                            }
+                            onClose();
+                        },
+                    },
+                ]);
+            } },
+            react_1.default.createElement(Close_1.default, null))) : (react_1.default.createElement(LockedPlugin, null)),
+        react_1.default.createElement(material_1.Typography, null, plugin.name)));
 });
 exports.default = InstalledPlugin;

package/dist/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/dist/PluginStoreWidget/components/InstalledPluginsList.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
 const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
 const InstalledPlugin_1 = __importDefault(require("./InstalledPlugin"));
 const InstalledPluginsList = (0, mobx_react_1.observer)(function InstalledPluginsList({ pluginManager, model, }) {
     const { plugins } = pluginManager;

package/dist/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/dist/PluginStoreWidget/components/PluginCard.js

@@ -27,16 +27,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const util_1 = require("@jbrowse/core/util");
 const types_1 = require("@jbrowse/core/util/types");
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-// icons
-const Person_1 = __importDefault(require("@mui/icons-material/Person"));
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 const Check_1 = __importDefault(require("@mui/icons-material/Check"));
+const Person_1 = __importDefault(require("@mui/icons-material/Person"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     card: {
         margin: '0.5em',
@@ -52,35 +50,39 @@ const useStyles = (0, mui_1.makeStyles)()({
         display: 'flex',
         alignItems: 'center',
     },
+    mr: {
+        marginRight: '0.5em',
+    },
 });
-const PluginCard = (0, mobx_react_1.observer)(function PluginCard({ plugin, model, adminMode, }) {
+const PluginCard = (0, mobx_react_1.observer)(function PluginCard({ plugin, model, }) {
     const { classes } = useStyles();
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.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] = (0, react_1.useState)(false);
-    const disableButton = isInstalled || tempDisabled;
-    const rootModel = (0, mobx_state_tree_1.getParent)(model, 3);
-    const { jbrowse } = rootModel;
-    return (react_1.default.createElement(material_1.Card, { variant: "outlined", key: plugin.name, className: classes.card },
+    const { adminMode, jbrowse } = session;
+    const { name, authors, description } = plugin;
+    return (react_1.default.createElement(material_1.Card, { variant: "outlined", key: name, className: classes.card },
         react_1.default.createElement(material_1.CardContent, null,
             react_1.default.createElement(material_1.Typography, { variant: "h5" },
                 react_1.default.createElement(material_1.Link, { href: `${plugin.location}#readme`, target: "_blank", rel: "noopener" }, plugin.name)),
             react_1.default.createElement("div", { className: classes.dataField },
-                react_1.default.createElement(Person_1.default, { style: { marginRight: '0.5em' } }),
-                react_1.default.createElement(material_1.Typography, null, plugin.authors.join(', '))),
+                react_1.default.createElement(Person_1.default, { className: classes.mr }),
+                react_1.default.createElement(material_1.Typography, null, authors.join(', '))),
             react_1.default.createElement(material_1.Typography, { className: classes.bold }, "Description:"),
-            react_1.default.createElement(material_1.Typography, null, plugin.description)),
+            react_1.default.createElement(material_1.Typography, null, description)),
         react_1.default.createElement(material_1.CardActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", disabled: disableButton, startIcon: isInstalled ? react_1.default.createElement(Check_1.default, null) : react_1.default.createElement(Add_1.default, null), onClick: () => {
+            react_1.default.createElement(material_1.Button, { variant: "contained", disabled: isInstalled || tempDisabled, startIcon: isInstalled ? react_1.default.createElement(Check_1.default, null) : react_1.default.createElement(Add_1.default, null), onClick: () => {
                     if (adminMode) {
-                        jbrowse.addPlugin({ name: plugin.name, url: plugin.url });
+                        jbrowse.addPlugin(plugin);
                     }
                     else if ((0, types_1.isSessionWithSessionPlugins)(session)) {
                         session.addSessionPlugin(plugin);
                     }
+                    else {
+                        session.notify('No way to install plugin');
+                    }
                     setTempDisabled(true);
                 } }, isInstalled ? 'Installed' : 'Install'))));
 });

package/dist/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/dist/PluginStoreWidget/components/PluginStoreWidget.js

@@ -27,21 +27,18 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
-const mobx_react_1 = require("mobx-react");
-const mobx_state_tree_1 = require("mobx-state-tree");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
-// icons
-const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
 const Clear_1 = __importDefault(require("@mui/icons-material/Clear"));
+const ExpandMore_1 = __importDefault(require("@mui/icons-material/ExpandMore"));
 const InfoOutlined_1 = __importDefault(require("@mui/icons-material/InfoOutlined"));
-// locals
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const mui_1 = require("tss-react/mui");
 const InstalledPluginsList_1 = __importDefault(require("./InstalledPluginsList"));
 const PluginCard_1 = __importDefault(require("./PluginCard"));
 const util_2 = require("./util");
-// lazies
 const AddCustomPluginDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./AddCustomPluginDialog'))));
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     expandIcon: {
@@ -58,53 +55,62 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         margin: '1em auto',
         display: 'flex',
     },
+    mr: {
+        marginRight: '0.3em',
+    },
+    m: {
+        margin: '1em',
+    },
 }));
 const PluginStoreWidget = (0, mobx_react_1.observer)(function ({ model, }) {
     const { classes } = useStyles();
     const { plugins, error } = (0, util_2.useFetchPlugins)();
-    const [open, setOpen] = (0, react_1.useState)(false);
-    const { adminMode } = (0, util_1.getSession)(model);
+    const session = (0, util_1.getSession)(model);
+    const { adminMode } = session;
     const { pluginManager } = (0, mobx_state_tree_1.getEnv)(model);
     return (react_1.default.createElement("div", null,
         adminMode && (react_1.default.createElement(react_1.default.Fragment, null,
             !util_1.isElectron && (react_1.default.createElement("div", { className: classes.adminBadge },
-                react_1.default.createElement(InfoOutlined_1.default, { style: { marginRight: '0.3em' } }),
+                react_1.default.createElement(InfoOutlined_1.default, { className: classes.mr }),
                 react_1.default.createElement(material_1.Typography, null,
                     "You are using the ",
                     react_1.default.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_1.default.createElement(material_1.Button, { className: classes.customPluginButton, variant: "contained", onClick: () => {
-                    setOpen(true);
-                } }, "Add custom plugin"),
-            open ? (react_1.default.createElement(react_1.Suspense, { fallback: null },
-                react_1.default.createElement(AddCustomPluginDialog, { onClose: () => {
-                        setOpen(false);
-                    }, model: model }))) : null)),
+                    session.queueDialog(onClose => [
+                        AddCustomPluginDialog,
+                        {
+                            model,
+                            onClose,
+                        },
+                    ]);
+                } }, "Add custom plugin"))),
         react_1.default.createElement(material_1.TextField, { label: "Filter plugins", value: model.filterText, onChange: event => {
                 model.setFilterText(event.target.value);
-            }, fullWidth: true, InputProps: {
-                endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
-                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
-                            model.clearFilterText();
-                        } },
-                        react_1.default.createElement(Clear_1.default, null)))),
+            }, fullWidth: true, slotProps: {
+                input: {
+                    endAdornment: (react_1.default.createElement(material_1.InputAdornment, { position: "end" },
+                        react_1.default.createElement(material_1.IconButton, { onClick: () => {
+                                model.clearFilterText();
+                            } },
+                            react_1.default.createElement(Clear_1.default, null)))),
+                },
             } }),
         react_1.default.createElement(material_1.Accordion, { defaultExpanded: true },
             react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
                 react_1.default.createElement(material_1.Typography, { variant: "h5" }, "Installed plugins")),
-            react_1.default.createElement("div", { style: { margin: '1em' } },
+            react_1.default.createElement("div", { className: classes.m },
                 react_1.default.createElement(InstalledPluginsList_1.default, { pluginManager: pluginManager, model: model }))),
         react_1.default.createElement(material_1.Accordion, { defaultExpanded: true },
             react_1.default.createElement(material_1.AccordionSummary, { expandIcon: react_1.default.createElement(ExpandMore_1.default, { className: classes.expandIcon }) },
                 react_1.default.createElement(material_1.Typography, { variant: "h5" }, "Available plugins")),
             error ? (react_1.default.createElement(material_1.Typography, { color: "error" }, `${error}`)) : plugins ? (plugins
                 .filter(plugin => {
-                // If plugin only has cjsUrl, don't display outside desktop
                 return (!(util_1.isElectron && plugin.cjsUrl) &&
                     plugin.name
                         .toLowerCase()
                         .includes(model.filterText.toLowerCase()));
             })
-                .map(plugin => (react_1.default.createElement(PluginCard_1.default, { key: plugin.name, plugin: plugin, model: model, adminMode: !!adminMode })))) : (react_1.default.createElement(ui_1.LoadingEllipses, null)))));
+                .map(plugin => (react_1.default.createElement(PluginCard_1.default, { key: plugin.name, plugin: plugin, model: model })))) : (react_1.default.createElement(ui_1.LoadingEllipses, null)))));
 });
 exports.default = PluginStoreWidget;

package/dist/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/dist/PluginStoreWidget/components/util.js

@@ -6,7 +6,6 @@ function useFetchPlugins() {
     const [plugins, setPlugins] = (0, react_1.useState)();
     const [error, setError] = (0, react_1.useState)();
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {

package/dist/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/dist/PluginStoreWidget/index.js

@@ -27,9 +27,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = PluginStoreWidgetF;
+const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const react_1 = require("react");
 const model_1 = __importDefault(require("./model"));
 const configSchema = (0, configuration_1.ConfigurationSchema)('PluginStoreWidget', {});
 function PluginStoreWidgetF(pluginManager) {

package/dist/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/dist/PluginStoreWidget/model.js

@@ -1,38 +1,20 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
     return mobx_state_tree_1.types
         .model('PluginStoreModel', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('PluginStoreWidget'),
-        /**
-         * #property
-         */
         filterText: '',
-        /**
-         * #property
-         */
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .actions(self => ({
-        /**
-         * #action
-         */
         clearFilterText() {
             self.filterText = '';
         },
-        /**
-         * #action
-         */
         setFilterText(newText) {
             self.filterText = newText;
         },

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

@@ -1,15 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const configuration_1 = require("@jbrowse/core/configuration");
-/**
- * #config UCSCTrackHubConnection
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+function x() { }
 const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTrackHubConnection', {
-    /**
-     * #slot
-     */
     hubTxtLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -18,18 +12,12 @@ const UCSCTrackHubConnection = (0, configuration_1.ConfigurationSchema)('UCSCTra
         },
         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: models_1.baseConnectionConfig,
 });
 exports.default = UCSCTrackHubConnection;

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

@@ -2,11 +2,11 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.doConnect = doConnect;
 const ucsc_hub_1 = require("@gmod/ucsc-hub");
-const ucscTrackHub_1 = require("./ucscTrackHub");
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
 const io_1 = require("@jbrowse/core/util/io");
 const nanoid_1 = require("@jbrowse/core/util/nanoid");
+const ucscTrackHub_1 = require("./ucscTrackHub");
 function resolve(uri, baseUri) {
     return new URL(uri, baseUri).href;
 }
@@ -17,7 +17,6 @@ async function doConnect(self) {
     try {
         const hubFileLocation = (0, configuration_1.getConf)(self, 'hubTxtLocation');
         const hubFileText = await (0, io_1.openLocation)(hubFileLocation).readFile('utf8');
-        // @ts-expect-error
         const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri);
         const { assemblyManager } = session;
         if (hubFileText.includes('useOneFile on')) {
@@ -26,7 +25,6 @@ async function doConnect(self) {
             const genomeName = genome.name;
             const asm = assemblyManager.get(genomeName);
             if (!asm) {
-                // @ts-expect-error
                 session.addSessionAssembly({
                     name: genomeName,
                     sequence: {
@@ -60,7 +58,6 @@ 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
                 ? {
@@ -83,7 +80,6 @@ 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/dist/{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/dist/{ucsc-trackhub → UCSCTrackHub}/index.js

@@ -5,15 +5,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = UCSCTrackHubConnectionF;
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const model_1 = __importDefault(require("./model"));
 const configSchema_1 = __importDefault(require("./configSchema"));
+const model_1 = __importDefault(require("./model"));
 function UCSCTrackHubConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => new pluggableElementTypes_1.ConnectionType({
-        name: 'UCSCTrackHubConnection',
-        configSchema: configSchema_1.default,
-        stateModel: (0, model_1.default)(pluginManager),
-        displayName: 'UCSC Track Hub',
-        description: 'A track or assembly hub in the Track Hub format',
-        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-    }));
+    pluginManager.addConnectionType(() => {
+        return new pluggableElementTypes_1.ConnectionType({
+            name: 'UCSCTrackHubConnection',
+            configSchema: configSchema_1.default,
+            stateModel: (0, model_1.default)(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',
+        });
+    });
 }