@jbrowse/plugin-data-management 2.18.0 → 3.0.0

package/dist/AddTrackWidget/components/util.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.categorizeAdapters = categorizeAdapters;
+function categorizeAdapters(adaptersList) {
+    var _a;
+    const map = {};
+    for (const adapter of adaptersList) {
+        const key = ((_a = adapter.adapterMetadata) === null || _a === void 0 ? void 0 : _a.category) || 'Default';
+        if (!map[key]) {
+            map[key] = [];
+        }
+        map[key].push(adapter);
+    }
+    return map;
+}

package/dist/AddTrackWidget/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };

package/dist/AddTrackWidget/model.d.ts

@@ -19,7 +19,9 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     adapterHint: string;
     textIndexTrack: boolean;
     textIndexingConf: IndexingAttr | undefined;
+    mixinData: {};
 } & {
+    setMixinData(arg: Record<string, unknown>): void;
     setAdapterHint(obj: string): void;
     setTrackSource(str: string): void;
     setTextIndexingConf(conf: IndexingAttr): void;
@@ -42,8 +44,19 @@ export default function f(pluginManager: PluginManager): import("mobx-state-tree
     readonly wrongProtocol: any;
     readonly unsupported: boolean;
     readonly assembly: any;
+    readonly trackAdapterType: string | undefined;
     readonly trackType: string;
 } & {
+    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/dist/AddTrackWidget/model.js

@@ -1,8 +1,14 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = f;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const mst_1 = require("@jbrowse/core/util/types/mst");
+const deepmerge_1 = __importDefault(require("deepmerge"));
 const mobx_state_tree_1 = require("mobx-state-tree");
 function isAbsoluteUrl(url = '') {
     try {
@@ -30,8 +36,12 @@ function f(pluginManager) {
         adapterHint: '',
         textIndexTrack: true,
         textIndexingConf: undefined,
+        mixinData: {},
     }))
         .actions(self => ({
+        setMixinData(arg) {
+            self.mixinData = arg;
+        },
         setAdapterHint(obj) {
             self.adapterHint = obj;
         },
@@ -120,14 +130,42 @@ function f(pluginManager) {
             var _a;
             return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
         },
+        get trackAdapterType() {
+            var _a;
+            return (_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type;
+        },
         get trackType() {
             return (self.altTrackType ||
-                (this.trackAdapter
-                    ? (0, tracks_1.guessTrackType)(this.trackAdapter.type, self)
+                (this.trackAdapterType
+                    ? (0, tracks_1.guessTrackType)(this.trackAdapterType, self)
                     : ''));
         },
     }))
         .views(self => ({
+        get trackConfig() {
+            const session = (0, util_1.getSession)(self);
+            const assemblyInstance = session.assemblyManager.get(self.assembly);
+            return assemblyInstance &&
+                self.trackAdapter &&
+                self.trackAdapter.type !== 'UNKNOWN'
+                ? (0, deepmerge_1.default)({
+                    trackId: [
+                        `${self.trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join(''),
+                    type: self.trackType,
+                    name: self.trackName,
+                    assemblyNames: [self.assembly],
+                    adapter: {
+                        ...self.trackAdapter,
+                        sequenceAdapter: (0, configuration_1.getConf)(assemblyInstance, [
+                            'sequence',
+                            'adapter',
+                        ]),
+                    },
+                }, self.mixinData)
+                : undefined;
+        },
         get warningMessage() {
             if (self.isFtp) {
                 return 'Warning: JBrowse cannot access files using the ftp protocol';
@@ -143,7 +181,9 @@ function f(pluginManager) {
           https URL for your track, or access the JBrowse app from the http
           protocol`;
             }
-            return '';
+            else {
+                return '';
+            }
         },
     }));
 }

package/dist/AssemblyManager/AssemblyAddForm.d.ts

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

package/dist/AssemblyManager/AssemblyAddForm.js

@@ -1,81 +1,42 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+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 AdapterSelector = (0, mobx_react_1.observer)(function ({ adapterSelection, setAdapterSelection, adapterTypes, }) {
-    return (react_1.default.createElement(material_1.TextField, { value: adapterSelection, variant: "outlined", select: true, helperText: "Type of adapter to use", fullWidth: true, onChange: event => {
+    return ((0, jsx_runtime_1.jsx)(material_1.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_1.default.createElement(material_1.MenuItem, { key: str, value: str }, str)))));
+        }, children: adapterTypes.map(str => ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { value: str, children: str }, str))) }));
 });
 const UnindexedFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, setFastaLocation, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Alert, { severity: "warning", style: { margin: 30 } }, "Note: use only relatively small files for this type, it is loaded into memory"),
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
-                    setFastaLocation(loc);
-                } }))));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Alert, { severity: "warning", style: { margin: 30 }, children: "Note: use only relatively small files for this type, it is loaded into memory" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } }) })] }));
 });
 const IndexedFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, faiLocation, setFaiLocation, setFastaLocation, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
-                    setFastaLocation(loc);
-                } })),
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
-                    setFaiLocation(loc);
-                } }))));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
+                        setFaiLocation(loc);
+                    } }) })] }));
 });
 const BgzipFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, faiLocation, gziLocation, setFaiLocation, setGziLocation, setFastaLocation, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
-                    setFastaLocation(loc);
-                } })),
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
-                    setFaiLocation(loc);
-                } })),
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "gziLocation", location: gziLocation, setLocation: loc => {
-                    setGziLocation(loc);
-                } }))));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+                        setFastaLocation(loc);
+                    } }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "faiLocation", location: faiLocation, setLocation: loc => {
+                        setFaiLocation(loc);
+                    } }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "gziLocation", location: gziLocation, setLocation: loc => {
+                        setGziLocation(loc);
+                    } }) })] }));
 });
 const TwoBitAdapterInput = (0, mobx_react_1.observer)(function ({ twoBitLocation, chromSizesLocation, setTwoBitLocation, setChromSizesLocation, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.FileSelector, { inline: true, name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
-                    setTwoBitLocation(loc);
-                } })),
-        react_1.default.createElement("div", null,
-            react_1.default.createElement(ui_1.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 ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
+                        setTwoBitLocation(loc);
+                    } }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: loc => {
+                        setChromSizesLocation(loc);
+                    } }) })] }));
 });
 const blank = { uri: '' };
 const adapterTypes = [
@@ -93,65 +54,57 @@ const AssemblyAddForm = (0, mobx_react_1.observer)(function ({ session, onClose,
     const [gziLocation, setGziLocation] = (0, react_1.useState)(blank);
     const [twoBitLocation, setTwoBitLocation] = (0, react_1.useState)(blank);
     const [chromSizesLocation, setChromSizesLocation] = (0, react_1.useState)(blank);
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement(material_1.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_1.default.createElement(material_1.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',
-                    },
-                } }),
-            react_1.default.createElement(AdapterSelector, { adapterSelection: adapterSelection, adapterTypes: adapterTypes, setAdapterSelection: setAdapterSelection }),
-            adapterSelection === 'IndexedFastaAdapter' ? (react_1.default.createElement(IndexedFastaAdapterInput, { fastaLocation: fastaLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'UnindexedFastaAdapter' ? (react_1.default.createElement(UnindexedFastaAdapterInput, { fastaLocation: fastaLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'TwoBitAdapter' ? (react_1.default.createElement(TwoBitAdapterInput, { twoBitLocation: twoBitLocation, chromSizesLocation: chromSizesLocation, setTwoBitLocation: setTwoBitLocation, setChromSizesLocation: setChromSizesLocation })) : (react_1.default.createElement(BgzipFastaAdapterInput, { fastaLocation: fastaLocation, gziLocation: gziLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setGziLocation: setGziLocation, setFastaLocation: setFastaLocation }))),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.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'
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)(material_1.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' },
+                        } }), (0, jsx_runtime_1.jsx)(material_1.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',
+                            },
+                        } }), (0, jsx_runtime_1.jsx)(AdapterSelector, { adapterSelection: adapterSelection, adapterTypes: adapterTypes, setAdapterSelection: setAdapterSelection }), adapterSelection === 'IndexedFastaAdapter' ? ((0, jsx_runtime_1.jsx)(IndexedFastaAdapterInput, { fastaLocation: fastaLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'UnindexedFastaAdapter' ? ((0, jsx_runtime_1.jsx)(UnindexedFastaAdapterInput, { fastaLocation: fastaLocation, setFastaLocation: setFastaLocation })) : adapterSelection === 'TwoBitAdapter' ? ((0, jsx_runtime_1.jsx)(TwoBitAdapterInput, { twoBitLocation: twoBitLocation, chromSizesLocation: chromSizesLocation, setTwoBitLocation: setTwoBitLocation, setChromSizesLocation: setChromSizesLocation })) : ((0, jsx_runtime_1.jsx)(BgzipFastaAdapterInput, { fastaLocation: fastaLocation, gziLocation: gziLocation, faiLocation: faiLocation, setFaiLocation: setFaiLocation, setGziLocation: setGziLocation, setFastaLocation: setFastaLocation }))] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.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: 'UnindexedFastaAdapter',
+                                                type: 'IndexedFastaAdapter',
                                                 fastaLocation,
+                                                faiLocation,
                                             }
-                                            : {
-                                                type: 'TwoBitAdapter',
-                                                twoBitLocation,
-                                                chromSizesLocation,
-                                            },
-                            },
-                        });
-                        session.notify(`Added "${assemblyName}"`, 'success');
-                    }
-                } }, "Submit"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
-                    onClose();
-                } }, "Cancel"))));
+                                            : adapterSelection === 'BgzipFastaAdapter'
+                                                ? {
+                                                    type: 'BgzipFastaAdapter',
+                                                    fastaLocation,
+                                                    faiLocation,
+                                                    gziLocation,
+                                                }
+                                                : adapterSelection === 'UnindexedFastaAdapter'
+                                                    ? {
+                                                        type: 'UnindexedFastaAdapter',
+                                                        fastaLocation,
+                                                    }
+                                                    : {
+                                                        type: 'TwoBitAdapter',
+                                                        twoBitLocation,
+                                                        chromSizesLocation,
+                                                    },
+                                    },
+                                });
+                                session.notify(`Added "${assemblyName}"`, 'success');
+                            }
+                        }, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                            onClose();
+                        }, children: "Cancel" })] })] }));
 });
 exports.default = AssemblyAddForm;

package/dist/AssemblyManager/AssemblyEditor.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 declare const AssemblyEditor: ({ assembly, onClose, }: {
     assembly?: AnyConfigurationModel;
     onClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyEditor;

package/dist/AssemblyManager/AssemblyEditor.js

@@ -1,9 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const plugin_config_1 = require("@jbrowse/plugin-config");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
@@ -16,12 +13,8 @@ const useStyles = (0, mui_1.makeStyles)()({
 });
 const AssemblyEditor = (0, mobx_react_1.observer)(function ({ assembly, onClose, }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement("div", { className: classes.container }, assembly ? (react_1.default.createElement(plugin_config_1.ConfigurationEditor, { model: { target: assembly } })) : (react_1.default.createElement("div", null, "No assembly")))),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    onClose();
-                } }, "Back"))));
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)("div", { className: classes.container, children: assembly ? ((0, jsx_runtime_1.jsx)(plugin_config_1.ConfigurationEditor, { model: { target: assembly } })) : ((0, jsx_runtime_1.jsx)("div", { children: "No assembly" })) }) }), (0, jsx_runtime_1.jsx)(material_1.DialogActions, { children: (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", onClick: () => {
+                        onClose();
+                    }, children: "Back" }) })] }));
 });
 exports.default = AssemblyEditor;

package/dist/AssemblyManager/AssemblyManager.d.ts

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

package/dist/AssemblyManager/AssemblyManager.js

@@ -1,32 +1,10 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
 const AssemblyAddForm_1 = __importDefault(require("./AssemblyAddForm"));
@@ -35,18 +13,18 @@ const AssemblyTable_1 = __importDefault(require("./AssemblyTable"));
 const AssemblyManager = (0, mobx_react_1.observer)(function ({ session, onClose, }) {
     const [isFormOpen, setFormOpen] = (0, react_1.useState)(false);
     const [editingAssembly, setEditingAssembly] = (0, react_1.useState)();
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, title: "Assembly manager", onClose: () => {
-            onClose();
-        } }, editingAssembly ? (react_1.default.createElement(AssemblyEditor_1.default, { assembly: editingAssembly, onClose: () => {
-            setEditingAssembly(undefined);
-        } })) : isFormOpen ? (react_1.default.createElement(AssemblyAddForm_1.default, { session: session, onClose: () => {
-            setFormOpen(false);
-        } })) : (react_1.default.createElement(AssemblyTable_1.default, { session: session, onClose: () => {
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Assembly manager", onClose: () => {
             onClose();
-        }, onAddAssembly: () => {
-            setFormOpen(true);
-        }, onEditAssembly: arg => {
-            setEditingAssembly(arg);
-        } }))));
+        }, children: editingAssembly ? ((0, jsx_runtime_1.jsx)(AssemblyEditor_1.default, { assembly: editingAssembly, onClose: () => {
+                setEditingAssembly(undefined);
+            } })) : isFormOpen ? ((0, jsx_runtime_1.jsx)(AssemblyAddForm_1.default, { session: session, onClose: () => {
+                setFormOpen(false);
+            } })) : ((0, jsx_runtime_1.jsx)(AssemblyTable_1.default, { session: session, onClose: () => {
+                onClose();
+            }, onAddAssembly: () => {
+                setFormOpen(true);
+            }, onEditAssembly: arg => {
+                setEditingAssembly(arg);
+            } })) }));
 });
 exports.default = AssemblyManager;

package/dist/AssemblyManager/AssemblyTable.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { AbstractSessionModel } from '@jbrowse/core/util';
 declare const AssemblyTable: ({ onEditAssembly, onAddAssembly, onClose, session, }: {
@@ -6,5 +5,5 @@ declare const AssemblyTable: ({ onEditAssembly, onAddAssembly, onClose, session,
     onAddAssembly: () => void;
     onClose: () => void;
     session: AbstractSessionModel;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyTable;

package/dist/AssemblyManager/AssemblyTable.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const configuration_1 = require("@jbrowse/core/configuration");
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
 const Create_1 = __importDefault(require("@mui/icons-material/Create"));
@@ -12,53 +12,41 @@ const material_1 = require("@mui/material");
 const x_data_grid_1 = require("@mui/x-data-grid");
 const mobx_react_1 = require("mobx-react");
 const AssemblyTable = (0, mobx_react_1.observer)(function ({ onEditAssembly, onAddAssembly, onClose, session, }) {
-    return (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement("div", { style: { display: 'flex', flexDirection: 'column' } },
-                react_1.default.createElement(x_data_grid_1.DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => {
-                        return {
+    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.DialogContent, { children: (0, jsx_runtime_1.jsx)("div", { style: { display: 'flex', flexDirection: 'column' }, children: (0, jsx_runtime_1.jsx)(x_data_grid_1.DataGrid, { rowHeight: 25, columnHeaderHeight: 35, hideFooter: session.assemblies.length < 25, rows: session.assemblies.map(assembly => ({
                             id: (0, configuration_1.readConfObject)(assembly, 'name'),
                             name: (0, configuration_1.readConfObject)(assembly, 'name'),
                             displayName: (0, configuration_1.readConfObject)(assembly, 'displayName'),
                             aliases: (0, configuration_1.readConfObject)(assembly, 'aliases'),
                             assembly,
-                        };
-                    }), columns: [
-                        { field: 'name' },
-                        { field: 'displayName' },
-                        { field: 'aliases' },
-                        {
-                            field: 'actions',
-                            renderCell: ({ row }) => {
-                                const { assembly, name } = row;
-                                const editable = session.sessionAssemblies.includes(assembly)
-                                    ? true
-                                    : session.adminMode;
-                                return (react_1.default.createElement(react_1.default.Fragment, null,
-                                    react_1.default.createElement(material_1.IconButton, { onClick: () => {
-                                            onEditAssembly(assembly);
-                                        } },
-                                        react_1.default.createElement(Create_1.default, null)),
-                                    react_1.default.createElement(material_1.IconButton, { "data-testid": `${name}-delete`, disabled: !editable, onClick: () => {
-                                            if (editable) {
-                                                if (!session.removeAssembly) {
-                                                    session.notify('Unable to find removeAssembly function');
-                                                }
-                                                else {
-                                                    session.removeAssembly(name);
-                                                }
-                                            }
-                                        } },
-                                        react_1.default.createElement(Delete_1.default, null))));
+                        })), columns: [
+                            { field: 'name' },
+                            { field: 'displayName' },
+                            { field: 'aliases' },
+                            {
+                                field: 'actions',
+                                renderCell: ({ row }) => {
+                                    const { assembly, name } = row;
+                                    const editable = session.sessionAssemblies.includes(assembly)
+                                        ? true
+                                        : session.adminMode;
+                                    return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.IconButton, { disabled: !editable, onClick: () => {
+                                                    onEditAssembly(assembly);
+                                                }, children: (0, jsx_runtime_1.jsx)(Create_1.default, {}) }), (0, jsx_runtime_1.jsx)(material_1.IconButton, { "data-testid": `${name}-delete`, disabled: !editable, onClick: () => {
+                                                    if (editable) {
+                                                        if (!session.removeAssembly) {
+                                                            session.notify('Unable to find removeAssembly function');
+                                                        }
+                                                        else {
+                                                            session.removeAssembly(name);
+                                                        }
+                                                    }
+                                                }, children: (0, jsx_runtime_1.jsx)(Delete_1.default, {}) })] }));
+                                },
                             },
-                        },
-                    ] }))),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                    onClose();
-                } }, "Close"),
-            react_1.default.createElement(material_1.Button, { variant: "contained", startIcon: react_1.default.createElement(Add_1.default, null), onClick: () => {
-                    onAddAssembly();
-                } }, "Add new assembly"))));
+                        ] }) }) }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
+                            onClose();
+                        }, children: "Close" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", startIcon: (0, jsx_runtime_1.jsx)(Add_1.default, {}), onClick: () => {
+                            onAddAssembly();
+                        }, children: "Add new assembly" })] })] }));
 });
 exports.default = AssemblyTable;