@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/esm/AddTrackWidget/model.d.ts

@@ -1,25 +1,13 @@
-import { Instance } from 'mobx-state-tree';
-import PluginManager from '@jbrowse/core/PluginManager';
-import { FileLocation } from '@jbrowse/core/util/types';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { FileLocation } from '@jbrowse/core/util/types';
+import type { Instance } from 'mobx-state-tree';
 interface IndexingAttr {
     attributes: string[];
     exclude: string[];
 }
-/**
- * #stateModel AddTrackModel
- */
 export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    /**
-     * #property
-     */
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    /**
-     * #property
-     */
     type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
-    /**
-     * #property
-     */
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
 }, {
     trackSource: string;
@@ -31,100 +19,44 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     adapterHint: string;
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
+    mixinData: {};
 } & {
-    /**
-     * #action
-     */
+    setMixinData(arg: Record<string, unknown>): void;
     setAdapterHint(obj: string): void;
-    /**
-     * #action
-     */
     setTrackSource(str: string): void;
-    /**
-     * #action
-     */
     setTextIndexingConf(conf: IndexingAttr): void;
-    /**
-     * #action
-     */
     setTextIndexTrack(flag: boolean): void;
-    /**
-     * #action
-     */
     setTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setIndexTrackData(obj: FileLocation): void;
-    /**
-     * #action
-     */
     setAssembly(str: string): void;
-    /**
-     * #action
-     */
     setTrackName(str: string): void;
-    /**
-     * #action
-     */
     setTrackType(str: string): void;
-    /**
-     * #action
-     */
     clearData(): void;
 } & {
-    /**
-     * #getter
-     */
     readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
-    /**
-     * #getter
-     */
     readonly trackName: string;
-    /**
-     * #getter
-     */
     readonly isFtp: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeTrackUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeIndexUrl: boolean;
-    /**
-     * #getter
-     */
     readonly isRelativeUrl: boolean;
-    /**
-     * #getter
-     */
     readonly trackHttp: any;
-    /**
-     * #getter
-     */
     readonly indexHttp: any;
-    /**
-     * #getter
-     */
     readonly wrongProtocol: any;
-    /**
-     * #getter
-     */
     readonly unsupported: boolean;
-    /**
-     * #getter
-     */
     readonly assembly: any;
-    /**
-     * #getter
-     */
+    readonly trackAdapterType: string | undefined;
     readonly trackType: string;
 } & {
-    /**
-     * #getter
-     */
+    readonly trackConfig: {
+        trackId: string;
+        type: string;
+        name: string;
+        assemblyNames: any[];
+        adapter: {
+            sequenceAdapter: any;
+            type: string;
+        };
+    } | undefined;
     readonly warningMessage: "" | "Warning: JBrowse cannot access files using the ftp protocol" | "Warning: one or more of your files do not provide the protocol e.g.\n          https://, please provide an absolute URL unless you are sure a\n          relative URL is intended." | "Warning: You entered a http:// resources but we cannot access HTTP\n          resources from JBrowse when it is running on https. Please use an\n          https URL for your track, or access the JBrowse app from the http\n          protocol";
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
 export type AddTrackStateModel = ReturnType<typeof f>;

package/esm/AddTrackWidget/model.js

@@ -1,6 +1,9 @@
-import { types } from 'mobx-state-tree';
+import { getConf } from '@jbrowse/core/configuration';
+import { getSession } from '@jbrowse/core/util';
+import { UNSUPPORTED, getFileName, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
 import { ElementId } from '@jbrowse/core/util/types/mst';
-import { guessAdapter, guessTrackType, getFileName, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
+import deepmerge from 'deepmerge';
+import { types } from 'mobx-state-tree';
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);
@@ -10,95 +13,56 @@ function isAbsoluteUrl(url = '') {
         return url.startsWith('/');
     }
 }
-/**
- * #stateModel AddTrackModel
- */
 export default function f(pluginManager) {
     return types
         .model('AddTrackModel', {
-        /**
-         * #property
-         */
         id: ElementId,
-        /**
-         * #property
-         */
         type: types.literal('AddTrackWidget'),
-        /**
-         * #property
-         */
         view: types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
         trackSource: 'fromFile',
         trackData: undefined,
         indexTrackData: undefined,
-        // alts
         altAssemblyName: '',
         altTrackName: '',
         altTrackType: '',
         adapterHint: '',
         textIndexTrack: true,
         textIndexingConf: undefined,
+        mixinData: {},
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
+        setMixinData(arg) {
+            self.mixinData = arg;
+        },
         setAdapterHint(obj) {
             self.adapterHint = obj;
         },
-        /**
-         * #action
-         */
         setTrackSource(str) {
             self.trackSource = str;
         },
-        /**
-         * #action
-         */
         setTextIndexingConf(conf) {
             self.textIndexingConf = conf;
         },
-        /**
-         * #action
-         */
         setTextIndexTrack(flag) {
             self.textIndexTrack = flag;
         },
-        /**
-         * #action
-         */
         setTrackData(obj) {
             self.trackData = obj;
         },
-        /**
-         * #action
-         */
         setIndexTrackData(obj) {
             self.indexTrackData = obj;
         },
-        /**
-         * #action
-         */
         setAssembly(str) {
             self.altAssemblyName = str;
         },
-        /**
-         * #action
-         */
         setTrackName(str) {
             self.altTrackName = str;
         },
-        /**
-         * #action
-         */
         setTrackType(str) {
             self.altTrackType = str;
         },
-        /**
-         * #action
-         */
         clearData() {
             self.trackSource = '';
             self.altTrackName = '';
@@ -112,107 +76,90 @@ export default function f(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get trackAdapter() {
             const { trackData, indexTrackData, adapterHint } = self;
             return trackData
                 ? guessAdapter(trackData, indexTrackData, adapterHint, self)
                 : undefined;
         },
-        /**
-         * #getter
-         */
         get trackName() {
             return (self.altTrackName ||
                 (self.trackData ? getFileName(self.trackData) : ''));
         },
-        /**
-         * #getter
-         */
         get isFtp() {
             var _a, _b;
             const { trackData: track, indexTrackData: index } = self;
-            return !!(
-            // @ts-expect-error
-            (((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
+            return !!((((_a = index === null || index === void 0 ? void 0 : index.uri) === null || _a === void 0 ? void 0 : _a.startsWith('ftp://')) || ((_b = track === null || track === void 0 ? void 0 : track.uri) === null || _b === void 0 ? void 0 : _b.startsWith('ftp://'))));
         },
-        /**
-         * #getter
-         */
         get isRelativeTrackUrl() {
             var _a;
-            // @ts-expect-error
             const uri = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
-        /**
-         * #getter
-         */
         get isRelativeIndexUrl() {
             var _a;
-            // @ts-expect-error
             const uri = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri;
             return uri ? !isAbsoluteUrl(uri) : false;
         },
-        /**
-         * #getter
-         */
         get isRelativeUrl() {
             return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
         },
-        /**
-         * #getter
-         */
         get trackHttp() {
             var _a, _b;
-            // @ts-expect-error
             return (_b = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
         },
-        /**
-         * #getter
-         */
         get indexHttp() {
             var _a, _b;
-            // @ts-expect-error
             return (_b = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
         },
-        /**
-         * #getter
-         */
         get wrongProtocol() {
             return (window.location.protocol === 'https:' &&
                 (this.trackHttp || this.indexHttp));
         },
-        /**
-         * #getter
-         */
         get unsupported() {
             var _a;
             return ((_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type) === UNSUPPORTED;
         },
-        /**
-         * #getter
-         */
         get assembly() {
             var _a;
             return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
         },
-        /**
-         * #getter
-         */
+        get trackAdapterType() {
+            var _a;
+            return (_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type;
+        },
         get trackType() {
             return (self.altTrackType ||
-                (this.trackAdapter
-                    ? guessTrackType(this.trackAdapter.type, self)
+                (this.trackAdapterType
+                    ? guessTrackType(this.trackAdapterType, self)
                     : ''));
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
+        get trackConfig() {
+            const session = getSession(self);
+            const assemblyInstance = session.assemblyManager.get(self.assembly);
+            return assemblyInstance &&
+                self.trackAdapter &&
+                self.trackAdapter.type !== 'UNKNOWN'
+                ? deepmerge({
+                    trackId: [
+                        `${self.trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join(''),
+                    type: self.trackType,
+                    name: self.trackName,
+                    assemblyNames: [self.assembly],
+                    adapter: {
+                        ...self.trackAdapter,
+                        sequenceAdapter: getConf(assemblyInstance, [
+                            'sequence',
+                            'adapter',
+                        ]),
+                    },
+                }, self.mixinData)
+                : undefined;
+        },
         get warningMessage() {
             if (self.isFtp) {
                 return 'Warning: JBrowse cannot access files using the ftp protocol';
@@ -228,7 +175,9 @@ export default function f(pluginManager) {
           https URL for your track, or access the JBrowse app from the http
           protocol`;
             }
-            return '';
+            else {
+                return '';
+            }
         },
     }));
 }

package/esm/AssemblyManager/AssemblyAddForm.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
-import { AbstractRootModel } from '@jbrowse/core/util/types';
-declare const AssemblyAddForm: ({ rootModel, setFormOpen, }: {
-    rootModel: AbstractRootModel;
-    setFormOpen: (arg: boolean) => void;
-}) => React.JSX.Element;
+import type { AbstractSessionModel } from '@jbrowse/core/util/types';
+declare const AssemblyAddForm: ({ session, onClose, }: {
+    session: AbstractSessionModel;
+    onClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyAddForm;

package/esm/AssemblyManager/AssemblyAddForm.js

@@ -1,51 +1,49 @@
-import React, { useState } from 'react';
-import { observer } from 'mobx-react';
-import { Button, Grid, MenuItem, Paper, TextField } from '@mui/material';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import { FileSelector } from '@jbrowse/core/ui';
-// icons
-import AddIcon from '@mui/icons-material/Add';
+import { Alert, Button, DialogActions, DialogContent, MenuItem, TextField, } from '@mui/material';
+import { observer } from 'mobx-react';
 const AdapterSelector = observer(function ({ adapterSelection, setAdapterSelection, adapterTypes, }) {
-    return (React.createElement(TextField, { value: adapterSelection, label: "Type", select: true, helperText: "Type of adapter to use", fullWidth: true, onChange: event => {
+    return (_jsx(TextField, { value: adapterSelection, variant: "outlined", select: true, helperText: "Type of adapter to use", fullWidth: true, onChange: event => {
             setAdapterSelection(event.target.value);
-        } }, adapterTypes.map(str => (React.createElement(MenuItem, { key: str, value: str }, str)))));
+        }, children: adapterTypes.map(str => (_jsx(MenuItem, { value: str, children: str }, str))) }));
+});
+const UnindexedFastaAdapterInput = observer(function ({ fastaLocation, setFastaLocation, }) {
+    return (_jsxs(_Fragment, { children: [_jsx(Alert, { severity: "warning", style: { margin: 30 }, children: "Note: use only relatively small files for this type, it is loaded into memory" }), _jsx("div", { children: _jsx(FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } }) })] }));
 });
-const AdapterInput = observer(function ({ adapterSelection, fastaLocation, faiLocation, gziLocation, twoBitLocation, chromSizesLocation, setFaiLocation, setGziLocation, setTwoBitLocation, setFastaLocation, setChromSizesLocation, }) {
-    if (adapterSelection === 'IndexedFastaAdapter' ||
-        adapterSelection === 'BgzipFastaAdapter') {
-        return (React.createElement(Grid, { container: true, spacing: 2 },
-            React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+const IndexedFastaAdapterInput = observer(function ({ fastaLocation, faiLocation, setFaiLocation, setFastaLocation, }) {
+    return (_jsxs(_Fragment, { children: [_jsx("div", { children: _jsx(FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
                         setFastaLocation(loc);
-                    } })),
-            React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "faiLocation", location: faiLocation, setLocation: loc => {
+                    } }) }), _jsx("div", { children: _jsx(FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
                         setFaiLocation(loc);
-                    } })),
-            adapterSelection === 'BgzipFastaAdapter' ? (React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "gziLocation", location: gziLocation, setLocation: loc => {
+                    } }) })] }));
+});
+const BgzipFastaAdapterInput = observer(function ({ fastaLocation, faiLocation, gziLocation, setFaiLocation, setGziLocation, setFastaLocation, }) {
+    return (_jsxs(_Fragment, { children: [_jsx("div", { children: _jsx(FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } }) }), _jsx("div", { children: _jsx(FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
+                        setFaiLocation(loc);
+                    } }) }), _jsx("div", { children: _jsx(FileSelector, { inline: true, name: "gziLocation", location: gziLocation, setLocation: loc => {
                         setGziLocation(loc);
-                    } }))) : null));
-    }
-    if (adapterSelection === 'TwoBitAdapter') {
-        return (React.createElement(Grid, { container: true, spacing: 2 },
-            React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
+                    } }) })] }));
+});
+const TwoBitAdapterInput = observer(function ({ twoBitLocation, chromSizesLocation, setTwoBitLocation, setChromSizesLocation, }) {
+    return (_jsxs(_Fragment, { children: [_jsx("div", { children: _jsx(FileSelector, { inline: true, name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
                         setTwoBitLocation(loc);
-                    } })),
-            React.createElement(Grid, { item: true },
-                React.createElement(FileSelector, { name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: loc => {
+                    } }) }), _jsx("div", { children: _jsx(FileSelector, { inline: true, name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: loc => {
                         setChromSizesLocation(loc);
-                    } }))));
-    }
-    return null;
+                    } }) })] }));
 });
 const blank = { uri: '' };
 const adapterTypes = [
     'IndexedFastaAdapter',
     'BgzipFastaAdapter',
+    'UnindexedFastaAdapter',
     'TwoBitAdapter',
 ];
-const AssemblyAddForm = observer(function ({ rootModel, setFormOpen, }) {
+const AssemblyAddForm = observer(function ({ session, onClose, }) {
     const [assemblyName, setAssemblyName] = useState('');
     const [assemblyDisplayName, setAssemblyDisplayName] = useState('');
     const [adapterSelection, setAdapterSelection] = useState(adapterTypes[0]);
@@ -54,75 +52,57 @@ const AssemblyAddForm = observer(function ({ rootModel, setFormOpen, }) {
     const [gziLocation, setGziLocation] = useState(blank);
     const [twoBitLocation, setTwoBitLocation] = useState(blank);
     const [chromSizesLocation, setChromSizesLocation] = useState(blank);
-    function createAssembly() {
-        var _a, _b;
-        if (assemblyName === '') {
-            (_a = rootModel.session) === null || _a === void 0 ? void 0 : _a.notify("Can't create an assembly without a name");
-        }
-        else {
-            setFormOpen(false);
-            let newAssembly;
-            if (adapterSelection === 'IndexedFastaAdapter') {
-                newAssembly = {
-                    name: assemblyName,
-                    displayName: assemblyDisplayName,
-                    sequence: {
-                        adapter: {
-                            type: 'IndexedFastaAdapter',
-                            fastaLocation,
-                            faiLocation,
-                        },
-                    },
-                };
-            }
-            else if (adapterSelection === 'BgzipFastaAdapter') {
-                newAssembly = {
-                    name: assemblyName,
-                    displayName: assemblyDisplayName,
-                    sequence: {
-                        adapter: {
-                            type: 'BgzipFastaAdapter',
-                            fastaLocation,
-                            faiLocation,
-                            gziLocation,
-                        },
-                    },
-                };
-            }
-            else if (adapterSelection === 'TwoBitAdapter') {
-                newAssembly = {
-                    name: assemblyName,
-                    displayName: assemblyDisplayName,
-                    sequence: {
-                        adapter: {
-                            type: 'TwoBitAdapter',
-                            twoBitLocation,
-                            chromSizesLocation,
-                        },
-                    },
-                };
-            }
-            else {
-                throw new Error(`unknown ${adapterSelection}`);
-            }
-            rootModel.jbrowse.addAssemblyConf(newAssembly);
-            (_b = rootModel.session) === null || _b === void 0 ? void 0 : _b.notify(`Successfully added ${assemblyName} assembly to JBrowse 2`, 'success');
-        }
-    }
-    return (React.createElement("div", null,
-        React.createElement(Paper, null,
-            React.createElement(TextField, { id: "assembly-name", label: "Assembly name", helperText: "The assembly name e.g. hg38", variant: "outlined", value: assemblyName, onChange: event => {
-                    setAssemblyName(event.target.value);
-                }, slotProps: {
-                    htmlInput: { 'data-testid': 'assembly-name' },
-                } }),
-            React.createElement(TextField, { id: "assembly-name", label: "Assembly display name", helperText: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: event => {
-                    setAssemblyDisplayName(event.target.value);
-                }, slotProps: {
-                    htmlInput: { 'data-testid': 'assembly-display-name' },
-                } }),
-            React.createElement(AdapterSelector, { adapterSelection: adapterSelection, adapterTypes: adapterTypes, setAdapterSelection: setAdapterSelection }),
-            React.createElement(AdapterInput, { adapterSelection: adapterSelection, fastaLocation: fastaLocation, faiLocation: faiLocation, gziLocation: gziLocation, twoBitLocation: twoBitLocation, chromSizesLocation: chromSizesLocation, setFaiLocation: setFaiLocation, setGziLocation: setGziLocation, setTwoBitLocation: setTwoBitLocation, setFastaLocation: setFastaLocation, setChromSizesLocation: setChromSizesLocation })),
-        React.createElement(Button, { variant: "contained", color: "secondary", startIcon: React.createElement(AddIcon, null), onClick: createAssembly }, "Create new assembly")));
+    return (_jsxs(_Fragment, { children: [_jsxs(DialogContent, { children: [_jsx(TextField, { id: "assembly-name", label: "Assembly name", helperText: "The assembly name e.g. hg38", variant: "outlined", value: assemblyName, onChange: event => {
+                            setAssemblyName(event.target.value);
+                        }, slotProps: {
+                            htmlInput: { 'data-testid': 'assembly-name' },
+                        } }), _jsx(TextField, { id: "assembly-name", label: "Assembly display name", helperText: '(optional) A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: event => {
+                            setAssemblyDisplayName(event.target.value);
+                        }, slotProps: {
+                            htmlInput: {
+                                'data-testid': 'assembly-display-name',
+                            },
+                        } }), _jsx(AdapterSelector, { adapterSelection: adapterSelection, adapterTypes: adapterTypes, setAdapterSelection: setAdapterSelection }), adapterSelection === 'IndexedFastaAdapter' ? (_jsx(IndexedFastaAdapterInput, { fastaLocation: fastaLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'UnindexedFastaAdapter' ? (_jsx(UnindexedFastaAdapterInput, { fastaLocation: fastaLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'TwoBitAdapter' ? (_jsx(TwoBitAdapterInput, { twoBitLocation: twoBitLocation, chromSizesLocation: chromSizesLocation, setTwoBitLocation: setTwoBitLocation, setChromSizesLocation: setChromSizesLocation })) : (_jsx(BgzipFastaAdapterInput, { fastaLocation: fastaLocation, gziLocation: gziLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setGziLocation: setGziLocation, setFastaLocation: setFastaLocation }))] }), _jsxs(DialogActions, { children: [_jsx(Button, { variant: "contained", color: "primary", onClick: () => {
+                            if (assemblyName === '') {
+                                session.notify("Can't create an assembly without a name");
+                            }
+                            else {
+                                onClose();
+                                session.addAssembly({
+                                    name: assemblyName,
+                                    displayName: assemblyDisplayName,
+                                    sequence: {
+                                        type: 'ReferenceSequenceTrack',
+                                        trackId: `${assemblyName}-${performance.now()}`,
+                                        adapter: adapterSelection === 'IndexedFastaAdapter'
+                                            ? {
+                                                type: 'IndexedFastaAdapter',
+                                                fastaLocation,
+                                                faiLocation,
+                                            }
+                                            : adapterSelection === 'BgzipFastaAdapter'
+                                                ? {
+                                                    type: 'BgzipFastaAdapter',
+                                                    fastaLocation,
+                                                    faiLocation,
+                                                    gziLocation,
+                                                }
+                                                : adapterSelection === 'UnindexedFastaAdapter'
+                                                    ? {
+                                                        type: 'UnindexedFastaAdapter',
+                                                        fastaLocation,
+                                                    }
+                                                    : {
+                                                        type: 'TwoBitAdapter',
+                                                        twoBitLocation,
+                                                        chromSizesLocation,
+                                                    },
+                                    },
+                                });
+                                session.notify(`Added "${assemblyName}"`, 'success');
+                            }
+                        }, children: "Submit" }), _jsx(Button, { variant: "contained", color: "secondary", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
 });
 export default AssemblyAddForm;

package/esm/AssemblyManager/AssemblyEditor.d.ts

@@ -1,6 +1,6 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-declare const AssemblyEditor: ({ assembly, }: {
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+declare const AssemblyEditor: ({ assembly, onClose, }: {
     assembly?: AnyConfigurationModel;
-}) => React.JSX.Element;
+    onClose: () => void;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyEditor;