@jbrowse/plugin-data-management 2.17.0 → 3.0.0

package/dist/AssemblyManager/AssemblyAddForm.js

@@ -1,79 +1,51 @@
 "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 mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
-// icons
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+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, label: "Type", 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 AdapterInput = (0, mobx_react_1.observer)(function ({ adapterSelection, fastaLocation, faiLocation, gziLocation, twoBitLocation, chromSizesLocation, setFaiLocation, setGziLocation, setTwoBitLocation, setFastaLocation, setChromSizesLocation, }) {
-    if (adapterSelection === 'IndexedFastaAdapter' ||
-        adapterSelection === 'BgzipFastaAdapter') {
-        return (react_1.default.createElement(material_1.Grid, { container: true, spacing: 2 },
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { name: "fastaLocation", location: fastaLocation, setLocation: loc => {
+const UnindexedFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, setFastaLocation, }) {
+    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);
-                    } })),
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { name: "faiLocation", location: faiLocation, setLocation: loc => {
+                    } }) })] }));
+});
+const IndexedFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, faiLocation, setFaiLocation, setFastaLocation, }) {
+    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);
-                    } })),
-            adapterSelection === 'BgzipFastaAdapter' ? (react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { name: "gziLocation", location: gziLocation, setLocation: loc => {
+                    } }) })] }));
+});
+const BgzipFastaAdapterInput = (0, mobx_react_1.observer)(function ({ fastaLocation, faiLocation, gziLocation, setFaiLocation, setGziLocation, setFastaLocation, }) {
+    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);
-                    } }))) : null));
-    }
-    if (adapterSelection === 'TwoBitAdapter') {
-        return (react_1.default.createElement(material_1.Grid, { container: true, spacing: 2 },
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { name: "twoBitLocation", location: twoBitLocation, setLocation: loc => {
+                    } }) })] }));
+});
+const TwoBitAdapterInput = (0, mobx_react_1.observer)(function ({ twoBitLocation, chromSizesLocation, setTwoBitLocation, setChromSizesLocation, }) {
+    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);
-                    } })),
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { name: "chromSizesLocation (optional, can be added to speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: 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);
-                    } }))));
-    }
-    return null;
+                    } }) })] }));
 });
 const blank = { uri: '' };
 const adapterTypes = [
     'IndexedFastaAdapter',
     'BgzipFastaAdapter',
+    'UnindexedFastaAdapter',
     'TwoBitAdapter',
 ];
-const AssemblyAddForm = (0, mobx_react_1.observer)(function ({ rootModel, setFormOpen, }) {
+const AssemblyAddForm = (0, mobx_react_1.observer)(function ({ session, onClose, }) {
     const [assemblyName, setAssemblyName] = (0, react_1.useState)('');
     const [assemblyDisplayName, setAssemblyDisplayName] = (0, react_1.useState)('');
     const [adapterSelection, setAdapterSelection] = (0, react_1.useState)(adapterTypes[0]);
@@ -82,75 +54,57 @@ const AssemblyAddForm = (0, mobx_react_1.observer)(function ({ rootModel, setFor
     const [gziLocation, setGziLocation] = (0, react_1.useState)(blank);
     const [twoBitLocation, setTwoBitLocation] = (0, react_1.useState)(blank);
     const [chromSizesLocation, setChromSizesLocation] = (0, react_1.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_1.default.createElement("div", null,
-        react_1.default.createElement(material_1.Paper, 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: '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 }),
-            react_1.default.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_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", startIcon: react_1.default.createElement(Add_1.default, null), onClick: createAssembly }, "Create new assembly")));
+    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}-${performance.now()}`,
+                                        adapter: adapterSelection === 'IndexedFastaAdapter'
+                                            ? {
+                                                type: 'IndexedFastaAdapter',
+                                                fastaLocation,
+                                                faiLocation,
+                                            }
+                                            : adapterSelection === 'BgzipFastaAdapter'
+                                                ? {
+                                                    type: 'BgzipFastaAdapter',
+                                                    fastaLocation,
+                                                    faiLocation,
+                                                    gziLocation,
+                                                }
+                                                : adapterSelection === 'UnindexedFastaAdapter'
+                                                    ? {
+                                                        type: 'UnindexedFastaAdapter',
+                                                        fastaLocation,
+                                                    }
+                                                    : {
+                                                        type: 'TwoBitAdapter',
+                                                        twoBitLocation,
+                                                        chromSizesLocation,
+                                                    },
+                                    },
+                                });
+                                session.notify(`Added "${assemblyName}"`, 'success');
+                            }
+                        }, children: "Submit" }), (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

@@ -1,6 +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;

package/dist/AssemblyManager/AssemblyEditor.js

@@ -1,11 +1,9 @@
 "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 mobx_react_1 = require("mobx-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");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     container: {
@@ -13,8 +11,10 @@ const useStyles = (0, mui_1.makeStyles)()({
         maxHeight: 600,
     },
 });
-const AssemblyEditor = (0, mobx_react_1.observer)(function ({ assembly, }) {
+const AssemblyEditor = (0, mobx_react_1.observer)(function ({ assembly, onClose, }) {
     const { classes } = useStyles();
-    return (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"))));
+    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

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

package/dist/AssemblyManager/AssemblyManager.js

@@ -1,66 +1,30 @@
 "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 mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
-// icons
-const Add_1 = __importDefault(require("@mui/icons-material/Add"));
-// locals
-const AssemblyTable_1 = __importDefault(require("./AssemblyTable"));
+const mobx_react_1 = require("mobx-react");
 const AssemblyAddForm_1 = __importDefault(require("./AssemblyAddForm"));
 const AssemblyEditor_1 = __importDefault(require("./AssemblyEditor"));
-const AssemblyManager = (0, mobx_react_1.observer)(function ({ rootModel, onClose, }) {
+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 [isAssemblyBeingEdited, setIsAssemblyBeingEdited] = (0, react_1.useState)(false);
-    const [assemblyBeingEdited, setAssemblyBeingEdited] = (0, react_1.useState)();
-    const showAssemblyTable = !isFormOpen && !isAssemblyBeingEdited;
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: () => {
-            onClose(false);
-        }, title: "Assembly manager" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            showAssemblyTable ? (react_1.default.createElement(AssemblyTable_1.default, { rootModel: rootModel, setIsAssemblyBeingEdited: setIsAssemblyBeingEdited, setAssemblyBeingEdited: setAssemblyBeingEdited })) : null,
-            isAssemblyBeingEdited ? (react_1.default.createElement(AssemblyEditor_1.default, { assembly: assemblyBeingEdited })) : null,
-            isFormOpen ? (react_1.default.createElement(AssemblyAddForm_1.default, { rootModel: rootModel, setFormOpen: setFormOpen })) : null),
-        react_1.default.createElement(material_1.DialogActions, null,
-            isFormOpen ? (react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    setFormOpen(false);
-                } }, "Back")) : null,
-            isAssemblyBeingEdited ? (react_1.default.createElement(material_1.Button, { variant: "contained", onClick: () => {
-                    setIsAssemblyBeingEdited(false);
-                } }, "Back")) : null,
-            showAssemblyTable ? (react_1.default.createElement(react_1.default.Fragment, null,
-                react_1.default.createElement(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                        onClose(false);
-                    } }, "Close"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", startIcon: react_1.default.createElement(Add_1.default, null), onClick: () => {
-                        setFormOpen(true);
-                    } }, "Add new assembly"))) : null)));
+    const [editingAssembly, setEditingAssembly] = (0, react_1.useState)();
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, title: "Assembly manager", onClose: () => {
+            onClose();
+        }, 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

@@ -1,13 +1,9 @@
-import React from 'react';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-declare const AssemblyTable: ({ rootModel, setIsAssemblyBeingEdited, setAssemblyBeingEdited, }: {
-    rootModel: {
-        jbrowse: {
-            removeAssemblyConf: (arg: string) => void;
-            assemblies: AnyConfigurationModel[];
-        };
-    };
-    setIsAssemblyBeingEdited(arg: boolean): void;
-    setAssemblyBeingEdited(arg: AnyConfigurationModel): void;
-}) => React.JSX.Element;
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AbstractSessionModel } from '@jbrowse/core/util';
+declare const AssemblyTable: ({ onEditAssembly, onAddAssembly, onClose, session, }: {
+    onEditAssembly: (arg: AnyConfigurationModel) => void;
+    onAddAssembly: () => void;
+    onClose: () => void;
+    session: AbstractSessionModel;
+}) => import("react/jsx-runtime").JSX.Element;
 export default AssemblyTable;

package/dist/AssemblyManager/AssemblyTable.js

@@ -3,43 +3,50 @@ 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 mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
+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"));
 const Delete_1 = __importDefault(require("@mui/icons-material/Delete"));
-const AssemblyTable = (0, mobx_react_1.observer)(function ({ rootModel, setIsAssemblyBeingEdited, setAssemblyBeingEdited, }) {
-    function removeAssembly(name) {
-        rootModel.jbrowse.removeAssemblyConf(name);
-    }
-    const { assemblies } = rootModel.jbrowse;
-    return (react_1.default.createElement(material_1.TableContainer, { component: material_1.Paper },
-        react_1.default.createElement(material_1.Table, null,
-            react_1.default.createElement(material_1.TableHead, null,
-                react_1.default.createElement(material_1.TableRow, null,
-                    react_1.default.createElement(material_1.TableCell, null, "Name"),
-                    react_1.default.createElement(material_1.TableCell, null, "Display name"),
-                    react_1.default.createElement(material_1.TableCell, null, "Aliases"),
-                    react_1.default.createElement(material_1.TableCell, null, "Actions"))),
-            react_1.default.createElement(material_1.TableBody, null, assemblies.map(assembly => {
-                const name = (0, configuration_1.readConfObject)(assembly, 'name');
-                const displayName = (0, configuration_1.readConfObject)(assembly, 'displayName');
-                const aliases = (0, configuration_1.readConfObject)(assembly, 'aliases');
-                return (react_1.default.createElement(material_1.TableRow, { key: name },
-                    react_1.default.createElement(material_1.TableCell, null, name),
-                    react_1.default.createElement(material_1.TableCell, null, displayName),
-                    react_1.default.createElement(material_1.TableCell, null, aliases ? aliases.toString() : ''),
-                    react_1.default.createElement(material_1.TableCell, null,
-                        react_1.default.createElement(material_1.IconButton, { "data-testid": `${name}-edit`, onClick: () => {
-                                setIsAssemblyBeingEdited(true);
-                                setAssemblyBeingEdited(assembly);
-                            } },
-                            react_1.default.createElement(Create_1.default, { color: "primary" })),
-                        react_1.default.createElement(material_1.IconButton, { "data-testid": `${name}-delete`, onClick: () => {
-                                removeAssembly(name);
-                            } },
-                            react_1.default.createElement(Delete_1.default, { color: "error" })))));
-            })))));
+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 ((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 ((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, {}) })] }));
+                                },
+                            },
+                        ] }) }) }), (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;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
-import { HierarchicalTrackSelectorModel } from '../model';
+import type { HierarchicalTrackSelectorModel } from '../model';
 declare const HierarchicalFab: ({ model, }: {
     model: HierarchicalTrackSelectorModel;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default HierarchicalFab;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalFab.js

@@ -1,38 +1,15 @@
 "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 material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
-const mobx_react_1 = require("mobx-react");
-// icons
 const Add_1 = __importDefault(require("@mui/icons-material/Add"));
+const material_1 = require("@mui/material");
+const mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
     fab: {
         position: 'absolute',
@@ -49,27 +26,22 @@ const HierarchicalFab = (0, mobx_react_1.observer)(function ({ model, }) {
     }
     const hasConnections = (0, util_1.isSessionModelWithConnections)(session);
     const hasAddTrack = (0, util_1.isSessionWithAddTracks)(session);
-    return hasAddTrack || hasConnections ? (react_1.default.createElement(react_1.default.Fragment, null,
-        react_1.default.createElement(material_1.Fab, { color: "secondary", className: classes.fab, onClick: event => {
-                setAnchorEl(event.currentTarget);
-            } },
-            react_1.default.createElement(Add_1.default, null)),
-        react_1.default.createElement(material_1.Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => {
-                setAnchorEl(null);
-            } },
-            hasConnections ? (react_1.default.createElement(material_1.MenuItem, { onClick: () => {
-                    handleFabClose();
-                    if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                        session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
-                    }
-                } }, "Add connection")) : null,
-            hasAddTrack ? (react_1.default.createElement(material_1.MenuItem, { onClick: () => {
-                    handleFabClose();
-                    if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                        session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
-                            view: model.view.id,
-                        }));
-                    }
-                } }, "Add track")) : null))) : null;
+    return hasAddTrack || hasConnections ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Fab, { color: "secondary", className: classes.fab, onClick: event => {
+                    setAnchorEl(event.currentTarget);
+                }, children: (0, jsx_runtime_1.jsx)(Add_1.default, {}) }), (0, jsx_runtime_1.jsxs)(material_1.Menu, { anchorEl: anchorEl, open: Boolean(anchorEl), onClose: () => {
+                    setAnchorEl(null);
+                }, children: [hasConnections ? ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { onClick: () => {
+                            handleFabClose();
+                            if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                                session.showWidget(session.addWidget('AddConnectionWidget', 'addConnectionWidget'));
+                            }
+                        }, children: "Add connection" })) : null, hasAddTrack ? ((0, jsx_runtime_1.jsx)(material_1.MenuItem, { onClick: () => {
+                            handleFabClose();
+                            if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                                session.showWidget(session.addWidget('AddTrackWidget', 'addTrackWidget', {
+                                    view: model.view.id,
+                                }));
+                            }
+                        }, children: "Add track" })) : null] })] })) : null;
 });
 exports.default = HierarchicalFab;

package/dist/HierarchicalTrackSelectorWidget/components/HierarchicalTrackSelector.d.ts

@@ -1,5 +1,4 @@
-import React from 'react';
-import { HierarchicalTrackSelectorModel } from '../model';
+import type { HierarchicalTrackSelectorModel } from '../model';
 declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overrideDimensions, }: {
     model: HierarchicalTrackSelectorModel;
     toolbarHeight: number;
@@ -7,5 +6,5 @@ declare const HierarchicalTrackSelectorContainer: ({ model, toolbarHeight, overr
         width: number;
         height: number;
     };
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default HierarchicalTrackSelectorContainer;