@jbrowse/plugin-data-management 2.17.0 → 2.18.0

package/dist/AddTrackWidget/model.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = f;
-const mobx_state_tree_1 = require("mobx-state-tree");
-const mst_1 = require("@jbrowse/core/util/types/mst");
 const tracks_1 = require("@jbrowse/core/util/tracks");
+const mst_1 = require("@jbrowse/core/util/types/mst");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function isAbsoluteUrl(url = '') {
     try {
         new URL(url);
@@ -13,30 +13,17 @@ function isAbsoluteUrl(url = '') {
         return url.startsWith('/');
     }
 }
-/**
- * #stateModel AddTrackModel
- */
 function f(pluginManager) {
     return mobx_state_tree_1.types
         .model('AddTrackModel', {
-        /**
-         * #property
-         */
         id: mst_1.ElementId,
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('AddTrackWidget'),
-        /**
-         * #property
-         */
         view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
     })
         .volatile(() => ({
         trackSource: 'fromFile',
         trackData: undefined,
         indexTrackData: undefined,
-        // alts
         altAssemblyName: '',
         altTrackName: '',
         altTrackType: '',
@@ -45,63 +32,33 @@ function f(pluginManager) {
         textIndexingConf: undefined,
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         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 = '';
@@ -115,96 +72,54 @@ function f(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get trackAdapter() {
             const { trackData, indexTrackData, adapterHint } = self;
             return trackData
                 ? (0, tracks_1.guessAdapter)(trackData, indexTrackData, adapterHint, self)
                 : undefined;
         },
-        /**
-         * #getter
-         */
         get trackName() {
             return (self.altTrackName ||
                 (self.trackData ? (0, tracks_1.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) === tracks_1.UNSUPPORTED;
         },
-        /**
-         * #getter
-         */
         get assembly() {
             var _a;
             return self.altAssemblyName || ((_a = self.view.assemblyNames) === null || _a === void 0 ? void 0 : _a[0]);
         },
-        /**
-         * #getter
-         */
         get trackType() {
             return (self.altTrackType ||
                 (this.trackAdapter
@@ -213,9 +128,6 @@ function f(pluginManager) {
         },
     }))
         .views(self => ({
-        /**
-         * #getter
-         */
         get warningMessage() {
             if (self.isFtp) {
                 return 'Warning: JBrowse cannot access files using the ftp protocol';

package/dist/AssemblyManager/AssemblyAddForm.d.ts

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

package/dist/AssemblyManager/AssemblyAddForm.js

@@ -22,58 +22,69 @@ var __importStar = (this && this.__importStar) || function (mod) {
     __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 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 (react_1.default.createElement(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)))));
 });
-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 => {
-                        setFastaLocation(loc);
-                    } })),
-            react_1.default.createElement(material_1.Grid, { item: true },
-                react_1.default.createElement(ui_1.FileSelector, { 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 => {
-                        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 => {
-                        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 => {
-                        setChromSizesLocation(loc);
-                    } }))));
-    }
-    return null;
+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);
+                } }))));
+});
+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);
+                } }))));
+});
+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);
+                } }))));
+});
+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);
+                } }))));
 });
 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 +93,65 @@ 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,
+    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: 'A human readable display name for the assembly e.g. "Homo sapiens (hg38)"', variant: "outlined", value: assemblyDisplayName, onChange: event => {
+            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' },
+                    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")));
+            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}-${performance.now()}`,
+                                adapter: adapterSelection === 'IndexedFastaAdapter'
+                                    ? {
+                                        type: 'IndexedFastaAdapter',
+                                        fastaLocation,
+                                        faiLocation,
+                                    }
+                                    : adapterSelection === 'BgzipFastaAdapter'
+                                        ? {
+                                            type: 'BgzipFastaAdapter',
+                                            fastaLocation,
+                                            faiLocation,
+                                            gziLocation,
+                                        }
+                                        : adapterSelection === 'UnindexedFastaAdapter'
+                                            ? {
+                                                type: 'UnindexedFastaAdapter',
+                                                fastaLocation,
+                                            }
+                                            : {
+                                                type: 'TwoBitAdapter',
+                                                twoBitLocation,
+                                                chromSizesLocation,
+                                            },
+                            },
+                        });
+                        session.notify(`Added "${assemblyName}"`, 'success');
+                    }
+                } }, "Submit"),
+            react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => {
+                    onClose();
+                } }, "Cancel"))));
 });
 exports.default = AssemblyAddForm;

package/dist/AssemblyManager/AssemblyEditor.d.ts

@@ -1,6 +1,7 @@
 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;
+    onClose: () => void;
 }) => React.JSX.Element;
 export default AssemblyEditor;

package/dist/AssemblyManager/AssemblyEditor.js

@@ -4,8 +4,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importDefault(require("react"));
-const mobx_react_1 = require("mobx-react");
 const 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 +14,14 @@ 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 (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"))));
 });
 exports.default = AssemblyEditor;

package/dist/AssemblyManager/AssemblyManager.d.ts

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

package/dist/AssemblyManager/AssemblyManager.js

@@ -27,40 +27,26 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const material_1 = require("@mui/material");
 const 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 (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: () => {
+            onClose();
+        }, onAddAssembly: () => {
+            setFormOpen(true);
+        }, onEditAssembly: arg => {
+            setEditingAssembly(arg);
+        } }))));
 });
 exports.default = AssemblyManager;

package/dist/AssemblyManager/AssemblyTable.d.ts

@@ -1,13 +1,10 @@
 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;
+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;
 }) => React.JSX.Element;
 export default AssemblyTable;