@jbrowse/plugin-data-management 3.7.0 → 4.0.1

package/esm/PluginStoreWidget/components/util.js

@@ -26,6 +26,6 @@ export function useFetchPlugins() {
 export function isSessionPlugin(plugin, session) {
     const { pluginManager } = getEnv(session);
     return isSessionWithSessionPlugins(session)
-        ? session.sessionPlugins.some(p => { var _a; return ((_a = pluginManager.pluginMetadata[plugin.name]) === null || _a === void 0 ? void 0 : _a.url) === p.url; })
+        ? session.sessionPlugins.some(p => pluginManager.pluginMetadata[plugin.name]?.url === p.url)
         : false;
 }

package/esm/PluginStoreWidget/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('PluginStoreWidget', {});
 export default function PluginStoreWidgetF(pluginManager) {
     pluginManager.addWidgetType(() => {
@@ -10,7 +10,7 @@ export default function PluginStoreWidgetF(pluginManager) {
             heading: 'Plugin store',
             configSchema,
             stateModel: stateModelFactory(pluginManager),
-            ReactComponent: lazy(() => import('./components/PluginStoreWidget')),
+            ReactComponent: lazy(() => import("./components/PluginStoreWidget.js")),
         });
     });
 }

package/esm/PluginStoreWidget/model.d.ts

@@ -1,13 +1,13 @@
 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>>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export default function stateModelFactory(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<"PluginStoreWidget">;
+    filterText: import("@jbrowse/mobx-state-tree").IType<string | undefined, string, string>;
+    view: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").IReferenceType<import("@jbrowse/mobx-state-tree").IAnyType>>;
 }, {
     clearFilterText(): void;
     setFilterText(newText: string): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type PluginStoreStateModel = ReturnType<typeof stateModelFactory>;
 export type PluginStoreModel = Instance<PluginStoreStateModel>;

package/esm/PluginStoreWidget/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 function stateModelFactory(pluginManager) {
     return types
         .model('PluginStoreModel', {

package/esm/UCSCTrackHubConnection/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const UCSCTrackHubConnection: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     hubTxtLocation: {
         type: string;
         defaultValue: {
@@ -12,7 +12,7 @@ declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/config
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         type: string;
         defaultValue: string;
@@ -23,5 +23,5 @@ declare const UCSCTrackHubConnection: import("@jbrowse/core/configuration/config
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
 export default UCSCTrackHubConnection;

package/esm/UCSCTrackHubConnection/doConnect.js

@@ -3,10 +3,9 @@ import { getConf } from '@jbrowse/core/configuration';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { nanoid } from '@jbrowse/core/util/nanoid';
-import { generateTracks } from './ucscTrackHub';
-import { fetchGenomesFile, fetchTrackDbFile, resolve } from './util';
+import { generateTracks } from "./ucscTrackHub.js";
+import { fetchGenomesFile, fetchTrackDbFile, resolve } from "./util.js";
 export async function doConnect(self) {
-    var _a;
     const { pluginManager } = getEnv(self);
     const session = getSession(self);
     const notLoadedAssemblies = [];
@@ -58,13 +57,10 @@ export async function doConnect(self) {
                         : {}),
                 });
             }
-            const asm2 = assemblyManager.get(genomeName);
-            const sequenceAdapter = getConf(asm2, ['sequence', 'adapter']);
             const tracksNew = generateTracks({
                 trackDb: tracks,
                 trackDbLoc: hubFileLocation,
                 assemblyName: genomeName,
-                sequenceAdapter,
                 baseUrl: hubUri,
             });
             self.addTrackConfs(tracksNew);
@@ -118,12 +114,10 @@ export async function doConnect(self) {
                         locationType: 'LocalPathLocation',
                     };
                 const trackDb = await fetchTrackDbFile(loc);
-                const sequenceAdapter = getConf(asm, ['sequence', 'adapter']);
                 const tracks = generateTracks({
                     trackDb,
                     trackDbLoc: loc,
                     assemblyName: genomeName,
-                    sequenceAdapter,
                     baseUrl: hubUri,
                 });
                 self.addTrackConfs(tracks);
@@ -144,6 +138,6 @@ export async function doConnect(self) {
     catch (e) {
         console.error(e);
         session.notifyError(`${getConf(self, 'name')}: "${e}"`, e);
-        (_a = session.breakConnection) === null || _a === void 0 ? void 0 : _a.call(session, self.configuration);
+        session.breakConnection?.(self.configuration);
     }
 }

package/esm/UCSCTrackHubConnection/index.js

@@ -1,6 +1,6 @@
 import { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
-import stateModelFactory from './model';
+import configSchema from "./configSchema.js";
+import stateModelFactory from "./model.js";
 export default function UCSCTrackHubConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => {
         return new ConnectionType({

package/esm/UCSCTrackHubConnection/model.d.ts

@@ -1,8 +1,8 @@
 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>;
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+export default function UCSCTrackHubConnection(pluginManager: PluginManager): import("@jbrowse/mobx-state-tree").IModelType<{
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    tracks: import("@jbrowse/mobx-state-tree").IArrayType<import("@jbrowse/mobx-state-tree").IAnyModelType>;
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         name: {
             type: string;
             defaultValue: string;
@@ -13,9 +13,9 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             defaultValue: never[];
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>;
 } & {
-    configuration: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    configuration: import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         hubTxtLocation: {
             type: string;
             defaultValue: {
@@ -29,7 +29,7 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             defaultValue: never[];
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaType<{
         name: {
             type: string;
             defaultValue: string;
@@ -40,36 +40,28 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager): im
             defaultValue: never[];
             description: string;
         };
-    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-    type: import("mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
+    }, import("node_modules/@jbrowse/core/src/configuration/configurationSchema.ts").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
+    type: import("@jbrowse/mobx-state-tree").ISimpleType<"UCSCTrackHubConnection">;
 }, {
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: ({
+    addTrackConf(trackConf: Record<string, unknown> | ({
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-    addTrackConfs(trackConfs: (({
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+    addTrackConfs(trackConfs: (Record<string, unknown> | ({
         [x: string]: any;
-    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+    } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
+        } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+    } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
     setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
     connect(): Promise<void>;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;

package/esm/UCSCTrackHubConnection/model.js

@@ -1,7 +1,7 @@
 import { ConfigurationReference } from '@jbrowse/core/configuration';
 import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
-import { types } from 'mobx-state-tree';
-import configSchema from './configSchema';
+import { types } from '@jbrowse/mobx-state-tree';
+import configSchema from "./configSchema.js";
 export default function UCSCTrackHubConnection(pluginManager) {
     return types
         .compose('UCSCTrackHubConnection', BaseConnectionModelFactory(pluginManager), types.model({
@@ -10,7 +10,7 @@ export default function UCSCTrackHubConnection(pluginManager) {
     }))
         .actions(self => ({
         async connect() {
-            const { doConnect } = await import('./doConnect');
+            const { doConnect } = await import("./doConnect.js");
             doConnect(self);
         },
     }));

package/esm/UCSCTrackHubConnection/ucscTrackHub.d.ts

@@ -1,10 +1,9 @@
 import type { TrackDbFile } from '@gmod/ucsc-hub';
 import type { FileLocation } from '@jbrowse/core/util';
-export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }: {
+export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, baseUrl, }: {
     trackDb: TrackDbFile;
     trackDbLoc: FileLocation;
     assemblyName: string;
-    sequenceAdapter: any;
     baseUrl: string;
 }): ({
     trackId: string;
@@ -36,7 +35,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         };
         cramLocation?: undefined;
         craiLocation?: undefined;
-        sequenceAdapter?: undefined;
         bigWigLocation?: undefined;
         bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
@@ -62,7 +60,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
             uri: string | undefined;
             locationType: string;
         };
-        sequenceAdapter: any;
         bamLocation?: undefined;
         index?: undefined;
         bigWigLocation?: undefined;
@@ -90,7 +87,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
-        sequenceAdapter?: undefined;
         bigBedLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
@@ -115,7 +111,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
-        sequenceAdapter?: undefined;
         bigWigLocation?: undefined;
         vcfGzLocation?: undefined;
         hicLocation?: undefined;
@@ -145,7 +140,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
-        sequenceAdapter?: undefined;
         bigWigLocation?: undefined;
         bigBedLocation?: undefined;
         hicLocation?: undefined;
@@ -170,7 +164,6 @@ export declare function generateTracks({ trackDb, trackDbLoc, assemblyName, sequ
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
-        sequenceAdapter?: undefined;
         bigWigLocation?: undefined;
         bigBedLocation?: undefined;
         vcfGzLocation?: undefined;

package/esm/UCSCTrackHubConnection/ucscTrackHub.js

@@ -1,7 +1,7 @@
 import { isUriLocation, notEmpty, objectHash } from '@jbrowse/core/util';
 import { generateUnknownTrackConf } from '@jbrowse/core/util/tracks';
-import { makeLoc2, makeLoc, makeLocAlt, resolve } from './util';
-export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdapter, baseUrl, }) {
+import { makeLoc2, makeLoc, makeLocAlt, resolve } from "./util.js";
+export function generateTracks({ trackDb, trackDbLoc, assemblyName, baseUrl, }) {
     const parentTrackKeys = new Set([
         'superTrack',
         'compositeTrack',
@@ -10,7 +10,6 @@ export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdap
     ]);
     return Object.entries(trackDb.data)
         .map(([trackName, track]) => {
-        var _a;
         const { data } = track;
         if (Object.keys(data).some(key => parentTrackKeys.has(key))) {
             return undefined;
@@ -19,7 +18,7 @@ export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdap
             const parentTracks = [];
             let currentTrackName = trackName;
             do {
-                currentTrackName = ((_a = trackDb.data[currentTrackName]) === null || _a === void 0 ? void 0 : _a.data.parent) || '';
+                currentTrackName = trackDb.data[currentTrackName]?.data.parent || '';
                 if (currentTrackName) {
                     currentTrackName = currentTrackName.split(' ')[0];
                     parentTracks.push(trackDb.data[currentTrackName]);
@@ -38,14 +37,13 @@ export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdap
                 category: [
                     track.data.group,
                     ...parentTracks
-                        .map(p => p === null || p === void 0 ? void 0 : p.data.group)
+                        .map(p => p?.data.group)
                         .filter((f) => !!f),
                 ].filter(f => !!f),
                 ...makeTrackConfig({
                     track,
                     trackDbLoc,
                     trackDb,
-                    sequenceAdapter,
                 }),
             };
         }
@@ -57,13 +55,12 @@ export function generateTracks({ trackDb, trackDbLoc, assemblyName, sequenceAdap
         assemblyNames: [assemblyName],
     }));
 }
-function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
-    var _a;
+function makeTrackConfig({ track, trackDbLoc, trackDb, }) {
     const { data } = track;
     const parent = data.parent || '';
     const bigDataUrl = data.bigDataUrl || '';
     const bigDataIdx = data.bigDataIndex || '';
-    const trackType = data.type || ((_a = trackDb.data[parent]) === null || _a === void 0 ? void 0 : _a.data.type) || '';
+    const trackType = data.type || trackDb.data[parent]?.data.type || '';
     const name = (data.shortLabel || '') + (bigDataUrl.includes('xeno') ? ' (xeno)' : '');
     const isUri = isUriLocation(trackDbLoc);
     let baseTrackType = trackType.split(' ')[0] || '';
@@ -100,7 +97,6 @@ function makeTrackConfig({ track, trackDbLoc, trackDb, sequenceAdapter, }) {
                 craiLocation: isUri
                     ? makeLocAlt(bigDataIdx, `${bigDataUrl}.crai`, trackDbLoc)
                     : makeLoc2(bigDataIdx, `${bigDataUrl}.crai`),
-                sequenceAdapter,
             },
         };
     }

package/esm/index.d.ts

@@ -16,5 +16,5 @@ export default class DataManagementPlugin extends Plugin {
     configure(_pluginManager: PluginManager): void;
 }
 export { AssemblyManager };
-export type { AddTrackModel } from './AddTrackWidget/model';
-export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget';
+export type { AddTrackModel } from './AddTrackWidget/model.ts';
+export type { HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget/index.ts';

package/esm/index.js

@@ -1,20 +1,17 @@
 import { lazy } from 'react';
 import Plugin from '@jbrowse/core/Plugin';
-import AddConnectionWidgetF from './AddConnectionWidget';
-import AddTrackWidgetF from './AddTrackWidget';
-import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget';
-import JB2TrackHubConnectionF from './JB2TrackHubConnection';
-import PluginStoreWidgetF from './PluginStoreWidget';
-import UCSCTrackHubConnectionF from './UCSCTrackHubConnection';
-const AssemblyManager = lazy(() => import('./AssemblyManager'));
+import AddConnectionWidgetF from "./AddConnectionWidget/index.js";
+import AddTrackWidgetF from "./AddTrackWidget/index.js";
+import HierarchicalTrackSelectorWidgetF from "./HierarchicalTrackSelectorWidget/index.js";
+import JB2TrackHubConnectionF from "./JB2TrackHubConnection/index.js";
+import PluginStoreWidgetF from "./PluginStoreWidget/index.js";
+import UCSCTrackHubConnectionF from "./UCSCTrackHubConnection/index.js";
+const AssemblyManager = lazy(() => import("./AssemblyManager/index.js"));
 export default class DataManagementPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'DataManagementPlugin';
-        this.exports = {
-            AssemblyManager,
-        };
-    }
+    name = 'DataManagementPlugin';
+    exports = {
+        AssemblyManager,
+    };
     install(pluginManager) {
         UCSCTrackHubConnectionF(pluginManager);
         JB2TrackHubConnectionF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-data-management",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 linear genome view",
   "keywords": [
     "jbrowse",
@@ -15,42 +15,22 @@
     "directory": "plugins/data-management"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/data-management",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/ucsc-hub": "^2.0.1",
-    "@jbrowse/core": "^3.7.0",
-    "@jbrowse/plugin-config": "^3.7.0",
-    "@jbrowse/product-core": "^3.7.0",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "@mui/x-data-grid": "^8.0.0",
+    "@gmod/ucsc-hub": "^2.0.3",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-data-grid": "^8.23.0",
     "deepmerge": "^4.3.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "react-virtualized-auto-sizer": "^1.0.26",
-    "react-vtree": "^3.0.0-beta.1",
-    "react-window": "^1.8.6",
-    "tss-react": "^4.0.0"
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/product-core": "^4.0.1",
+    "@jbrowse/core": "^4.0.1",
+    "@jbrowse/plugin-config": "^4.0.1"
   },
   "peerDependencies": {
     "react": ">=18.0.0"
@@ -58,8 +38,19 @@
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/data-management",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/AddConnectionWidget/components/AddConnectionWidget.d.ts

@@ -1,4 +0,0 @@
-declare const AddConnectionWidget: ({ model }: {
-    model: unknown;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AddConnectionWidget;

package/dist/AddConnectionWidget/components/AddConnectionWidget.js

@@ -1,66 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const util_1 = require("@jbrowse/core/util");
-const product_core_1 = require("@jbrowse/product-core");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const mui_1 = require("tss-react/mui");
-const ConfigureConnection_1 = __importDefault(require("./ConfigureConnection"));
-const ConnectionTypeSelect_1 = __importDefault(require("./ConnectionTypeSelect"));
-const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    root: {
-        marginTop: theme.spacing(1),
-    },
-    stepper: {
-        backgroundColor: theme.palette.background.default,
-    },
-    button: {
-        marginTop: theme.spacing(1),
-        marginRight: theme.spacing(1),
-    },
-    actionsContainer: {
-        marginBottom: theme.spacing(2),
-    },
-}));
-const steps = ['Select a Connection Type', 'Configure Connection'];
-const AddConnectionWidget = (0, mobx_react_1.observer)(function ({ model }) {
-    const [connectionType, setConnectionType] = (0, react_1.useState)();
-    const [connectionId, setConnectionId] = (0, react_1.useState)();
-    const [activeStep, setActiveStep] = (0, react_1.useState)(0);
-    const { classes } = useStyles();
-    const session = (0, util_1.getSession)(model);
-    const { pluginManager } = (0, util_1.getEnv)(session);
-    const configModel = (0, react_1.useMemo)(() => connectionType === null || connectionType === void 0 ? void 0 : connectionType.configSchema.create({ connectionId }, (0, util_1.getEnv)(model)), [connectionId, connectionType, model]);
-    return ((0, jsx_runtime_1.jsx)("div", { className: classes.root, children: (0, jsx_runtime_1.jsx)(material_1.Stepper, { className: classes.stepper, activeStep: activeStep, orientation: "vertical", children: steps.map(label => ((0, jsx_runtime_1.jsxs)(material_1.Step, { children: [(0, jsx_runtime_1.jsx)(material_1.StepLabel, { children: label }), (0, jsx_runtime_1.jsxs)(material_1.StepContent, { children: [activeStep === 0 ? ((0, jsx_runtime_1.jsx)(ConnectionTypeSelect_1.default, { connectionTypeChoices: pluginManager.getConnectionElements(), connectionType: connectionType, setConnectionType: c => {
-                                    setConnectionType(c);
-                                    if (!c) {
-                                        return;
-                                    }
-                                    setConnectionId(`${c.name}-${Date.now()}`);
-                                } })) : connectionType && configModel ? ((0, jsx_runtime_1.jsx)(ConfigureConnection_1.default, { connectionType: connectionType, model: configModel, session: session })) : null, (0, jsx_runtime_1.jsxs)("div", { className: classes.actionsContainer, children: [(0, jsx_runtime_1.jsx)(material_1.Button, { disabled: activeStep === 0, onClick: () => {
-                                            setActiveStep(activeStep - 1);
-                                        }, className: classes.button, children: "Back" }), (0, jsx_runtime_1.jsx)(material_1.Button, { disabled: !((activeStep === 0 && connectionType) ||
-                                            (activeStep === 1 && configModel)), variant: "contained", color: "primary", onClick: () => {
-                                            if (activeStep === steps.length - 1) {
-                                                if (configModel && (0, product_core_1.isSessionWithConnections)(session)) {
-                                                    const conf = session.addConnectionConf(configModel);
-                                                    session.makeConnection(conf);
-                                                }
-                                                else {
-                                                    session.notify('No config model to add');
-                                                }
-                                                if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                                                    session.hideWidget(model);
-                                                }
-                                            }
-                                            else {
-                                                setActiveStep(activeStep + 1);
-                                            }
-                                        }, className: classes.button, "data-testid": "addConnectionNext", children: activeStep === steps.length - 1 ? 'Connect' : 'Next' })] })] })] }, label))) }) }));
-});
-exports.default = AddConnectionWidget;

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

@@ -1,9 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-import type { AbstractSessionModel } from '@jbrowse/core/util';
-declare const ConfigureConnection: ({ connectionType, model, session, }: {
-    connectionType: ConnectionType;
-    model: AnyConfigurationModel;
-    session: AbstractSessionModel;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ConfigureConnection;

package/dist/AddConnectionWidget/components/ConfigureConnection.js

@@ -1,12 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const plugin_config_1 = require("@jbrowse/plugin-config");
-const mobx_react_1 = require("mobx-react");
-const ConfigureConnection = (0, mobx_react_1.observer)(function ({ connectionType, model, session, }) {
-    const ConfigEditorComponent = connectionType.configEditorComponent || plugin_config_1.ConfigurationEditor;
-    return ((0, jsx_runtime_1.jsx)(react_1.Suspense, { fallback: (0, jsx_runtime_1.jsx)(ui_1.LoadingEllipses, {}), children: (0, jsx_runtime_1.jsx)(ConfigEditorComponent, { model: { target: model }, session: session }) }));
-});
-exports.default = ConfigureConnection;

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

@@ -1,7 +0,0 @@
-import type { ConnectionType } from '@jbrowse/core/pluggableElementTypes';
-declare const ConnectionTypeSelect: ({ connectionTypeChoices, connectionType, setConnectionType, }: {
-    connectionTypeChoices: ConnectionType[];
-    connectionType?: ConnectionType;
-    setConnectionType: (c?: ConnectionType) => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default ConnectionTypeSelect;

package/dist/AddConnectionWidget/components/ConnectionTypeSelect.js

@@ -1,19 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const ConnectionTypeSelect = (0, mobx_react_1.observer)(function ConnectionTypeSelect({ connectionTypeChoices, connectionType, setConnectionType, }) {
-    const firstChoice = connectionTypeChoices[0];
-    (0, react_1.useEffect)(() => {
-        if (!connectionType) {
-            setConnectionType(firstChoice);
-        }
-    }, [connectionType, firstChoice, setConnectionType]);
-    return ((0, jsx_runtime_1.jsx)("form", { autoComplete: "off", children: connectionType ? ((0, jsx_runtime_1.jsx)(material_1.TextField, { value: connectionType.name, label: "connectionType", helperText: connectionType.description ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [connectionType.description, connectionType.url ? ((0, jsx_runtime_1.jsx)(ui_1.ExternalLink, { href: connectionType.url })) : null] })) : null, select: true, fullWidth: true, onChange: event => {
-                setConnectionType(connectionTypeChoices.find(c => c.name === event.target.value));
-            }, variant: "outlined", children: connectionTypeChoices.map(c => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: c.name, children: c.displayName || c.name }, c.name))) })) : null }));
-});
-exports.default = ConnectionTypeSelect;

package/dist/AddConnectionWidget/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function AddConnectionWidgetF(pluginManager: PluginManager): void;