@jbrowse/plugin-data-management 3.7.0 → 4.0.0

package/dist/AddTrackWidget/components/doSubmit.js

@@ -1,55 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.doSubmit = doSubmit;
-const util_1 = require("@jbrowse/core/util");
-const mobx_state_tree_1 = require("mobx-state-tree");
-function doTextIndexTrack({ trackId, model, }) {
-    const { textIndexingConf, trackName, assembly } = model;
-    const { jobsManager } = (0, mobx_state_tree_1.getRoot)(model);
-    const attr = textIndexingConf || {
-        attributes: ['Name', 'ID'],
-        exclude: ['CDS', 'exon'],
-    };
-    const indexName = `${trackName}-index`;
-    jobsManager.queueJob({
-        indexingParams: {
-            ...attr,
-            assemblies: [assembly],
-            tracks: [trackId],
-            indexType: 'perTrack',
-            name: indexName,
-            timestamp: new Date().toISOString(),
-        },
-        name: indexName,
-        cancelCallback: () => jobsManager.abortJob(),
-    });
-}
-function doSubmit({ model }) {
-    var _a;
-    const { textIndexTrack, trackAdapter, view } = model;
-    const session = (0, util_1.getSession)(model);
-    const trackConfig = model.getTrackConfig(Date.now());
-    if (!(0, util_1.isSessionWithAddTracks)(session)) {
-        throw new Error("Can't add tracks to this session");
-    }
-    else if (trackConfig && trackAdapter) {
-        const { trackId } = trackConfig;
-        session.addTrackConf(trackConfig);
-        (_a = view === null || view === void 0 ? void 0 : view.showTrack) === null || _a === void 0 ? void 0 : _a.call(view, trackId);
-        if (util_1.isElectron &&
-            textIndexTrack &&
-            (0, util_1.isSupportedIndexingAdapter)(trackAdapter.type)) {
-            doTextIndexTrack({
-                model,
-                trackId,
-            });
-        }
-        model.clearData();
-        if ((0, util_1.isSessionModelWithWidgets)(session)) {
-            session.hideWidget(model);
-        }
-    }
-    else {
-        throw new Error('Failed to add track.\nThe configuration of this file is not currently supported.');
-    }
-}

package/dist/AddTrackWidget/components/util.d.ts

@@ -1,2 +0,0 @@
-import type { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-export declare function categorizeAdapters(adaptersList: AdapterType[]): Record<string, AdapterType[]>;

package/dist/AddTrackWidget/components/util.js

@@ -1,15 +0,0 @@
-"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.d.ts

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

package/dist/AddTrackWidget/index.js

@@ -1,55 +0,0 @@
-"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 () {
-    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 };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = AddTrackWidgetF;
-const react_1 = require("react");
-const configuration_1 = require("@jbrowse/core/configuration");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-const model_1 = __importDefault(require("./model"));
-const configSchema = (0, configuration_1.ConfigurationSchema)('AddTrackWidget', {});
-function AddTrackWidgetF(pluginManager) {
-    pluginManager.addWidgetType(() => {
-        return new pluggableElementTypes_1.WidgetType({
-            name: 'AddTrackWidget',
-            heading: 'Add a track',
-            configSchema,
-            stateModel: (0, model_1.default)(pluginManager),
-            ReactComponent: (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/AddTrackWidget')))),
-        });
-    });
-}

package/dist/AddTrackWidget/model.d.ts

@@ -1,64 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-import type { FileLocation } from '@jbrowse/core/util/types';
-import type { Instance } from 'mobx-state-tree';
-interface IndexingAttr {
-    attributes: string[];
-    exclude: string[];
-}
-export default function f(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
-    id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    type: import("mobx-state-tree").ISimpleType<"AddTrackWidget">;
-    view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
-}, {
-    trackSource: string;
-    trackData: FileLocation | undefined;
-    indexTrackData: FileLocation | undefined;
-    altAssemblyName: string;
-    altTrackName: string;
-    altTrackType: string;
-    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;
-    setTextIndexTrack(flag: boolean): void;
-    setTrackData(obj: FileLocation): void;
-    setIndexTrackData(obj: FileLocation): void;
-    setAssembly(str: string): void;
-    setTrackName(str: string): void;
-    setTrackType(str: string): void;
-    clearData(): void;
-} & {
-    readonly trackAdapter: import("@jbrowse/core/util/tracks").AdapterConfig | undefined;
-    readonly trackName: string;
-    readonly isFtp: boolean;
-    readonly isRelativeTrackUrl: boolean;
-    readonly isRelativeIndexUrl: boolean;
-    readonly isRelativeUrl: boolean;
-    readonly trackHttp: any;
-    readonly indexHttp: any;
-    readonly wrongProtocol: any;
-    readonly unsupported: boolean;
-    readonly assembly: any;
-    readonly trackAdapterType: string | undefined;
-    readonly trackType: string;
-} & {
-    getTrackConfig(timestamp: number): {
-        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>;
-export type AddTrackModel = Instance<AddTrackStateModel>;
-export {};

package/dist/AddTrackWidget/model.js

@@ -1,190 +0,0 @@
-"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 {
-        new URL(url);
-        return true;
-    }
-    catch (error) {
-        return url.startsWith('/');
-    }
-}
-function f(pluginManager) {
-    return mobx_state_tree_1.types
-        .model('AddTrackModel', {
-        id: mst_1.ElementId,
-        type: mobx_state_tree_1.types.literal('AddTrackWidget'),
-        view: mobx_state_tree_1.types.safeReference(pluginManager.pluggableMstType('view', 'stateModel')),
-    })
-        .volatile(() => ({
-        trackSource: 'fromFile',
-        trackData: undefined,
-        indexTrackData: undefined,
-        altAssemblyName: '',
-        altTrackName: '',
-        altTrackType: '',
-        adapterHint: '',
-        textIndexTrack: true,
-        textIndexingConf: undefined,
-        mixinData: {},
-    }))
-        .actions(self => ({
-        setMixinData(arg) {
-            self.mixinData = arg;
-        },
-        setAdapterHint(obj) {
-            self.adapterHint = obj;
-        },
-        setTrackSource(str) {
-            self.trackSource = str;
-        },
-        setTextIndexingConf(conf) {
-            self.textIndexingConf = conf;
-        },
-        setTextIndexTrack(flag) {
-            self.textIndexTrack = flag;
-        },
-        setTrackData(obj) {
-            self.trackData = obj;
-            self.adapterHint = '';
-        },
-        setIndexTrackData(obj) {
-            self.indexTrackData = obj;
-        },
-        setAssembly(str) {
-            self.altAssemblyName = str;
-        },
-        setTrackName(str) {
-            self.altTrackName = str;
-        },
-        setTrackType(str) {
-            self.altTrackType = str;
-        },
-        clearData() {
-            self.trackSource = '';
-            self.altTrackName = '';
-            self.altTrackType = '';
-            self.altAssemblyName = '';
-            self.adapterHint = '';
-            self.indexTrackData = undefined;
-            self.trackData = undefined;
-            self.textIndexingConf = undefined;
-            self.textIndexTrack = true;
-        },
-    }))
-        .views(self => ({
-        get trackAdapter() {
-            const { trackData, indexTrackData, adapterHint } = self;
-            return trackData
-                ? (0, tracks_1.guessAdapter)(trackData, indexTrackData, adapterHint, self)
-                : undefined;
-        },
-        get trackName() {
-            return (self.altTrackName ||
-                (self.trackData ? (0, tracks_1.getFileName)(self.trackData) : ''));
-        },
-        get isFtp() {
-            var _a, _b;
-            const { trackData: track, indexTrackData: index } = self;
-            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://'))));
-        },
-        get isRelativeTrackUrl() {
-            var _a;
-            const uri = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri;
-            return uri ? !isAbsoluteUrl(uri) : false;
-        },
-        get isRelativeIndexUrl() {
-            var _a;
-            const uri = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri;
-            return uri ? !isAbsoluteUrl(uri) : false;
-        },
-        get isRelativeUrl() {
-            return this.isRelativeIndexUrl || this.isRelativeTrackUrl;
-        },
-        get trackHttp() {
-            var _a, _b;
-            return (_b = (_a = self.trackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
-        },
-        get indexHttp() {
-            var _a, _b;
-            return (_b = (_a = self.indexTrackData) === null || _a === void 0 ? void 0 : _a.uri) === null || _b === void 0 ? void 0 : _b.startsWith('http://');
-        },
-        get wrongProtocol() {
-            return (window.location.protocol === 'https:' &&
-                (this.trackHttp || this.indexHttp));
-        },
-        get unsupported() {
-            var _a;
-            return ((_a = this.trackAdapter) === null || _a === void 0 ? void 0 : _a.type) === tracks_1.UNSUPPORTED;
-        },
-        get assembly() {
-            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.trackAdapterType
-                    ? (0, tracks_1.guessTrackType)(this.trackAdapterType, self)
-                    : ''));
-        },
-    }))
-        .views(self => ({
-        getTrackConfig(timestamp) {
-            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: [
-                        `${self.trackName.toLowerCase().replaceAll(' ', '_')}-${timestamp}`,
-                        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';
-            }
-            else if (self.isRelativeUrl) {
-                return `Warning: one or more of your files do not provide the protocol e.g.
-          https://, please provide an absolute URL unless you are sure a
-          relative URL is intended.`;
-            }
-            else if (self.wrongProtocol) {
-                return `Warning: You entered a http:// resources but we cannot access HTTP
-          resources from JBrowse when it is running on https. Please use an
-          https URL for your track, or access the JBrowse app from the http
-          protocol`;
-            }
-            else {
-                return '';
-            }
-        },
-    }));
-}

package/dist/AssemblyManager/AssemblyAddForm.d.ts

@@ -1,6 +0,0 @@
-import type { AbstractSessionModel } from '@jbrowse/core/util/types';
-declare const AssemblyAddForm: ({ session, onClose, }: {
-    session: AbstractSessionModel;
-    onClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AssemblyAddForm;

package/dist/AssemblyManager/AssemblyAddForm.js

@@ -1,94 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const material_1 = require("@mui/material");
-const mobx_react_1 = require("mobx-react");
-const AdapterSelector = (0, mobx_react_1.observer)(function ({ adapterSelection, setAdapterSelection, adapterTypes, }) {
-    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);
-        }, 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 ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(material_1.Alert, { severity: "warning", style: { margin: 8 }, children: "Note: a FASTA index will be generated on submit, might take a couple minutes and if the file is remote, it will be downloaded in full" }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "FASTA file", location: fastaLocation, setLocation: setFastaLocation }) })] }));
-});
-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: "FASTA file", location: fastaLocation, setLocation: setFastaLocation }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "FASTA index (.fai) file", location: faiLocation, setLocation: setFaiLocation }) })] }));
-});
-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: "FASTA file (.fa.gz)", location: fastaLocation, setLocation: setFastaLocation }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "FASTA index (.fai) file", location: faiLocation, setLocation: setFaiLocation }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: "FASTA gzip index (.gzi) file", location: gziLocation, setLocation: setGziLocation }) })] }));
-});
-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: "2bit file", location: twoBitLocation, setLocation: setTwoBitLocation }) }), (0, jsx_runtime_1.jsx)("div", { children: (0, jsx_runtime_1.jsx)(ui_1.FileSelector, { inline: true, name: ".chrom.sizes (optional, can speed up loading 2bit files with many contigs)", location: chromSizesLocation, setLocation: setChromSizesLocation }) })] }));
-});
-const blank = { uri: '' };
-const adapterTypes = [
-    'IndexedFastaAdapter',
-    'BgzipFastaAdapter',
-    'UnindexedFastaAdapter',
-    'TwoBitAdapter',
-];
-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]);
-    const [fastaLocation, setFastaLocation] = (0, react_1.useState)(blank);
-    const [faiLocation, setFaiLocation] = (0, react_1.useState)(blank);
-    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 ((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-display-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 +0,0 @@
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-declare const AssemblyEditor: ({ assembly, onClose, }: {
-    assembly?: AnyConfigurationModel;
-    onClose: () => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default AssemblyEditor;

package/dist/AssemblyManager/AssemblyEditor.js

@@ -1,20 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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: {
-        overflow: 'auto',
-        maxHeight: 600,
-    },
-});
-const AssemblyEditor = (0, mobx_react_1.observer)(function ({ assembly, onClose, }) {
-    const { classes } = useStyles();
-    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 +0,0 @@
-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

@@ -1,30 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const ui_1 = require("@jbrowse/core/ui");
-const mobx_react_1 = require("mobx-react");
-const AssemblyAddForm_1 = __importDefault(require("./AssemblyAddForm"));
-const AssemblyEditor_1 = __importDefault(require("./AssemblyEditor"));
-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 ((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

@@ -1,9 +0,0 @@
-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

@@ -1,53 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const configuration_1 = require("@jbrowse/core/configuration");
-const DataGridFlexContainer_1 = __importDefault(require("@jbrowse/core/ui/DataGridFlexContainer"));
-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 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)(DataGridFlexContainer_1.default, { 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/AssemblyManager/index.d.ts

@@ -1 +0,0 @@
-export { default } from './AssemblyManager';

package/dist/AssemblyManager/index.js

@@ -1,8 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = void 0;
-var AssemblyManager_1 = require("./AssemblyManager");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(AssemblyManager_1).default; } });

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

@@ -1,5 +0,0 @@
-import type { HierarchicalTrackSelectorModel } from '../model';
-declare const HierarchicalFab: ({ model, }: {
-    model: HierarchicalTrackSelectorModel;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default HierarchicalFab;