@jbrowse/plugin-spreadsheet-view 3.6.5 → 4.0.0

package/esm/SpreadsheetView/components/SpreadsheetViewActual.js

@@ -1,9 +1,9 @@
 import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
 import { useState } from 'react';
 import { ResizeHandle } from '@jbrowse/core/ui';
+import { makeStyles } from '@jbrowse/core/util/tss-react';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-import SpreadsheetDataGrid from './SpreadsheetDataGrid';
+import SpreadsheetDataGrid from "./SpreadsheetDataGrid.js";
 const useStyles = makeStyles()(theme => ({
     contentArea: {
         overflow: 'auto',
@@ -18,7 +18,7 @@ const useStyles = makeStyles()(theme => ({
         borderTop: '1px solid #fafafa',
     },
 }));
-const SpreadsheetViewActual = observer(function ({ model, }) {
+const SpreadsheetViewActual = observer(function SpreadsheetViewActual({ model, }) {
     const [initialHeight, setInitialHeight] = useState(0);
     const { classes } = useStyles();
     const { spreadsheet, hideVerticalResizeHandle, height } = model;

package/esm/SpreadsheetView/components/TrackSelector.d.ts

@@ -1,4 +1,4 @@
-import type { ImportWizardModel } from '../ImportWizard';
+import type { ImportWizardModel } from '../ImportWizard.ts';
 declare const TrackSelector: ({ model, selectedAssembly, }: {
     model: ImportWizardModel;
     selectedAssembly: string;

package/esm/SpreadsheetView/components/TrackSelector.js

@@ -4,21 +4,20 @@ import { ErrorMessage } from '@jbrowse/core/ui';
 import { coarseStripHTML } from '@jbrowse/core/util';
 import { MenuItem, TextField } from '@mui/material';
 import { observer } from 'mobx-react';
-const TrackSelector = observer(function ({ model, selectedAssembly, }) {
-    var _a;
+const TrackSelector = observer(function TrackSelector({ model, selectedAssembly, }) {
     const filteredTracks = selectedAssembly
         ? model.tracksForAssembly(selectedAssembly)
         : undefined;
-    const resetTrack = ((_a = filteredTracks === null || filteredTracks === void 0 ? void 0 : filteredTracks[0]) === null || _a === void 0 ? void 0 : _a.track.trackId) || '';
+    const resetTrack = filteredTracks?.[0]?.track.trackId || '';
     const [selectedTrack, setSelectedTrack] = useState(resetTrack);
     useEffect(() => {
-        const entry = filteredTracks === null || filteredTracks === void 0 ? void 0 : filteredTracks.find(f => selectedTrack === f.track.trackId);
+        const entry = filteredTracks?.find(f => selectedTrack === f.track.trackId);
         if (entry) {
             model.setFileSource(entry.loc);
             model.setFileType(entry.type);
         }
     }, [model, selectedTrack, filteredTracks]);
-    return (_jsx("div", { children: (filteredTracks === null || filteredTracks === void 0 ? void 0 : filteredTracks.length) ? (_jsx(TextField, { select: true, label: "Tracks", variant: "outlined", value: selectedTrack, onChange: event => {
+    return (_jsx("div", { children: filteredTracks?.length ? (_jsx(TextField, { select: true, label: "Tracks", variant: "outlined", value: selectedTrack, onChange: event => {
                 setSelectedTrack(event.target.value);
             }, children: filteredTracks.map(({ track, label }) => (_jsx(MenuItem, { value: track.trackId, children: coarseStripHTML(label) }, track.trackId))) })) : (_jsx(ErrorMessage, { error: `No tracks found for ${selectedAssembly}` })) }));
 });

package/esm/SpreadsheetView/importAdapters/BedImport.js

@@ -1,15 +1,14 @@
-import { isNumber } from './isNumber';
-import { bufferToLines, parseStrand } from './util';
+import { isNumber } from "./isNumber.js";
+import { bufferToLines, parseStrand } from "./util.js";
 export function parseBedBuffer(buffer) {
-    var _a;
     const lines = bufferToLines(buffer);
     const rest = lines.filter(line => !(line.startsWith('#') ||
         line.startsWith('browser') ||
         line.startsWith('track')));
     const lastHeaderLine = lines.findLast(line => line.startsWith('#'));
     const coreColumns = ['refName', 'start', 'end'];
-    const numExtraColumns = Math.max(0, (((_a = rest[0]) === null || _a === void 0 ? void 0 : _a.split('\t').length) || 0) - coreColumns.length);
-    const extraNames = (lastHeaderLine === null || lastHeaderLine === void 0 ? void 0 : lastHeaderLine.includes('\t'))
+    const numExtraColumns = Math.max(0, (rest[0]?.split('\t').length || 0) - coreColumns.length);
+    const extraNames = lastHeaderLine?.includes('\t')
         ? lastHeaderLine
             .slice(1)
             .split('\t')

package/esm/SpreadsheetView/importAdapters/BedpeImport.js

@@ -1,7 +1,6 @@
 import { isNumber } from '@mui/x-data-grid/internals';
-import { bufferToLines, parseStrand } from './util';
+import { bufferToLines, parseStrand } from "./util.js";
 export function parseBedPEBuffer(buffer) {
-    var _a;
     const lines = bufferToLines(buffer);
     const rest = lines.filter(line => !(line.startsWith('#') ||
         line.startsWith('browser') ||
@@ -19,8 +18,8 @@ export function parseBedPEBuffer(buffer) {
         'strand',
         'mateStrand',
     ];
-    const numExtraColumns = Math.max(0, (((_a = rest[0]) === null || _a === void 0 ? void 0 : _a.split('\t').length) || 0) - coreColumns.length);
-    const extraNames = (lastHeaderLine === null || lastHeaderLine === void 0 ? void 0 : lastHeaderLine.includes('\t'))
+    const numExtraColumns = Math.max(0, (rest[0]?.split('\t').length || 0) - coreColumns.length);
+    const extraNames = lastHeaderLine?.includes('\t')
         ? lastHeaderLine
             .slice(1)
             .split('\t')

package/esm/SpreadsheetView/importAdapters/STARFusionImport.js

@@ -1,5 +1,5 @@
-import { isNumber } from './isNumber';
-import { bufferToLines, parseStrand } from './util';
+import { isNumber } from "./isNumber.js";
+import { bufferToLines, parseStrand } from "./util.js";
 function parseSTARFusionBreakpointString(str) {
     const fields = str.split(':');
     return {

package/esm/SpreadsheetView/importAdapters/VcfImport.js

@@ -1,7 +1,7 @@
 import VCF from '@gmod/vcf';
 import { VcfFeature } from '@jbrowse/plugin-variants';
-import { isNumber } from './isNumber';
-import { bufferToLines } from './util';
+import { isNumber } from "./isNumber.js";
+import { bufferToLines } from "./util.js";
 export function parseVcfBuffer(buffer) {
     const lines = bufferToLines(buffer);
     const header = lines.filter(l => l.startsWith('#')).join('\n');
@@ -12,13 +12,15 @@ export function parseVcfBuffer(buffer) {
     let i = 0;
     for (const line of body) {
         const [CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, ...rest] = line.split('\t');
-        const ret = Object.fromEntries((INFO === null || INFO === void 0 ? void 0 : INFO.split(';').map(f => f.trim()).map(e => {
+        const ret = Object.fromEntries(INFO?.split(';')
+            .map(f => f.trim())
+            .map(e => {
             const [key, val = 'true'] = e.split('=');
             const k = `INFO.${key.trim()}`;
             keys.add(k);
             const v = val.trim();
             return [k, isNumber(v) ? +v : v];
-        })) || []);
+        }) || []);
         rows.push({
             cellData: {
                 CHROM,

package/esm/SpreadsheetView/index.d.ts

@@ -1,3 +1,3 @@
 import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SpreadsheetViewF(pluginManager: PluginManager): void;
-export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel';
+export type { SpreadsheetViewModel, SpreadsheetViewStateModel, } from './SpreadsheetViewModel.ts';

package/esm/SpreadsheetView/index.js

@@ -1,13 +1,13 @@
 import { lazy } from 'react';
 import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import stateModelFactory from './SpreadsheetViewModel';
+import stateModelFactory from "./SpreadsheetViewModel.js";
 export default function SpreadsheetViewF(pluginManager) {
     pluginManager.addViewType(() => {
         return new ViewType({
             name: 'SpreadsheetView',
             displayName: 'Spreadsheet view',
             stateModel: stateModelFactory(),
-            ReactComponent: lazy(() => import('./components/SpreadsheetView')),
+            ReactComponent: lazy(() => import("./components/SpreadsheetView.js")),
         });
     });
 }

package/esm/index.d.ts

@@ -5,4 +5,4 @@ export default class SpreadsheetViewPlugin extends Plugin {
     install(pluginManager: PluginManager): void;
     configure(pluginManager: PluginManager): void;
 }
-export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './SpreadsheetView';
+export { type SpreadsheetViewModel, type SpreadsheetViewStateModel, } from './SpreadsheetView/index.ts';

package/esm/index.js

@@ -1,13 +1,10 @@
 import Plugin from '@jbrowse/core/Plugin';
 import { isAbstractMenuManager } from '@jbrowse/core/util';
 import ViewComfyIcon from '@mui/icons-material/ViewComfy';
-import LaunchSpreadsheetViewF from './LaunchSpreadsheetView';
-import SpreadsheetViewF from './SpreadsheetView';
+import LaunchSpreadsheetViewF from "./LaunchSpreadsheetView/index.js";
+import SpreadsheetViewF from "./SpreadsheetView/index.js";
 export default class SpreadsheetViewPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'SpreadsheetViewPlugin';
-    }
+    name = 'SpreadsheetViewPlugin';
     install(pluginManager) {
         SpreadsheetViewF(pluginManager);
         LaunchSpreadsheetViewF(pluginManager);
@@ -25,3 +22,4 @@ export default class SpreadsheetViewPlugin extends Plugin {
         }
     }
 }
+export {} from "./SpreadsheetView/index.js";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-spreadsheet-view",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 spreadsheet view",
   "keywords": [
     "jbrowse",
@@ -15,50 +15,43 @@
     "directory": "plugins/spreadsheet-view"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/spreadsheet-view",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.6.5",
-    "@jbrowse/plugin-linear-genome-view": "^3.6.5",
-    "@jbrowse/plugin-variants": "^3.6.5",
-    "@mui/icons-material": "^7.0.0",
-    "@mui/material": "^7.0.0",
-    "@mui/x-data-grid": "^8.0.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "tss-react": "^4.0.0"
+    "@gmod/vcf": "^6.1.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/icons-material": "^7.3.6",
+    "@mui/material": "^7.3.6",
+    "@mui/x-data-grid": "^8.23.0",
+    "mobx": "^6.15.0",
+    "mobx-react": "^9.2.1",
+    "@jbrowse/plugin-linear-genome-view": "^4.0.0",
+    "@jbrowse/core": "^4.0.0",
+    "@jbrowse/sv-core": "^4.0.0",
+    "@jbrowse/plugin-variants": "^4.0.0"
   },
   "peerDependencies": {
     "react": ">=18.0.0",
     "react-dom": ">=18.0.0"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/spreadsheet-view",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/LaunchSpreadsheetView/index.d.ts

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

package/dist/LaunchSpreadsheetView/index.js

@@ -1,21 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = LaunchSpreadsheetViewF;
-function LaunchSpreadsheetViewF(pluginManager) {
-    pluginManager.addToExtensionPoint('LaunchView-SpreadsheetView', async ({ session, assembly, uri, fileType, }) => {
-        var _a, _b;
-        const view = session.addView('SpreadsheetView');
-        const exts = uri.split('.');
-        let ext = (_a = exts.pop()) === null || _a === void 0 ? void 0 : _a.toUpperCase();
-        if (ext === 'GZ') {
-            ext = (_b = exts.pop()) === null || _b === void 0 ? void 0 : _b.toUpperCase();
-        }
-        view.importWizard.setFileType(fileType || ext || '');
-        view.importWizard.setSelectedAssemblyName(assembly);
-        view.importWizard.setFileSource({
-            uri,
-            locationType: 'UriLocation',
-        });
-        await view.importWizard.import(assembly);
-    });
-}

package/dist/SpreadsheetView/ImportWizard.d.ts

@@ -1,51 +0,0 @@
-import type { FileLocation } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
-export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
-    fileType: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
-    hasColumnNameLine: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
-    columnNameLineNumber: import("mobx-state-tree").IType<number | undefined, number, number>;
-    selectedAssemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    cachedFileLocation: import("mobx-state-tree").IType<FileLocation | undefined, FileLocation | undefined, FileLocation | undefined>;
-}, {
-    fileTypes: string[];
-    fileSource: any;
-    error: unknown;
-    loading: boolean;
-} & {
-    readonly isReadyToOpen: any;
-    readonly fileName: any;
-    readonly requiresUnzip: any;
-    isValidRefName(refName: string, assemblyName?: string): boolean;
-    tracksForAssembly(selectedAssembly: string): {
-        track: {
-            [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                [x: string]: any;
-            } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
-                setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
-                    [x: string]: any;
-                } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-            } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-        } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
-        label: string;
-        assemblyNames: any;
-        type: string;
-        loc: FileLocation;
-    }[];
-} & {
-    setSelectedAssemblyName(s: string): void;
-    setFileSource(newSource: unknown): void;
-    setColumnNameLineNumber(newnumber: number): void;
-    setFileType(typeName: string): void;
-    setError(error: unknown): void;
-    setLoading(arg: boolean): void;
-    cancelButton(): void;
-    setCachedFileHandle(arg: FileLocation): void;
-} & {
-    import(assemblyName: string): Promise<void>;
-} & {
-    afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
-export type ImportWizardStateModel = ReturnType<typeof stateModelFactory>;
-export type ImportWizardModel = Instance<ImportWizardStateModel>;

package/dist/SpreadsheetView/ImportWizard.js

@@ -1,250 +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;
-    };
-})();
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = stateModelFactory;
-const configuration_1 = require("@jbrowse/core/configuration");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const tracks_1 = require("@jbrowse/core/util/tracks");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const IMPORT_SIZE_LIMIT = 100000000;
-const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'];
-const fileTypeParsers = {
-    VCF: () => Promise.resolve().then(() => __importStar(require('./importAdapters/VcfImport'))).then(r => r.parseVcfBuffer),
-    BED: () => Promise.resolve().then(() => __importStar(require('./importAdapters/BedImport'))).then(r => r.parseBedBuffer),
-    BEDPE: () => Promise.resolve().then(() => __importStar(require('./importAdapters/BedpeImport'))).then(r => r.parseBedPEBuffer),
-    'STAR-Fusion': () => Promise.resolve().then(() => __importStar(require('./importAdapters/STARFusionImport'))).then(r => r.parseSTARFusionBuffer),
-};
-function getType(adapter) {
-    if (adapter.vcfLocation || adapter.vcfGzLocation) {
-        return 'VCF';
-    }
-    else if (adapter.bedLocation || adapter.bedGzLocation) {
-        return 'BED';
-    }
-    else if (adapter.bedpeLocation) {
-        return 'BEDPE';
-    }
-    else {
-        return undefined;
-    }
-}
-function getAdapterLoc(adapter) {
-    return (adapter.vcfLocation ||
-        adapter.vcfGzLocation ||
-        adapter.bedLocation ||
-        adapter.bedGzLocation ||
-        adapter.bedpeLocation);
-}
-const fileTypesRegexp = new RegExp(`\\.(${fileTypes.join('|')})(\\.gz)?$`, 'i');
-function x() { }
-function stateModelFactory() {
-    return mobx_state_tree_1.types
-        .model('SpreadsheetImportWizard', {
-        fileType: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.enumeration(fileTypes), 'VCF'),
-        hasColumnNameLine: true,
-        columnNameLineNumber: 1,
-        selectedAssemblyName: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.string),
-        cachedFileLocation: mobx_state_tree_1.types.frozen(),
-    })
-        .volatile(() => ({
-        fileTypes,
-        fileSource: undefined,
-        error: undefined,
-        loading: false,
-    }))
-        .views(self => ({
-        get isReadyToOpen() {
-            return (self.fileSource &&
-                (self.fileSource.blobId ||
-                    self.fileSource.localPath ||
-                    self.fileSource.uri));
-        },
-        get fileName() {
-            return (self.fileSource.uri ||
-                self.fileSource.localPath ||
-                (self.fileSource.blobId && self.fileSource.name));
-        },
-        get requiresUnzip() {
-            return this.fileName.endsWith('gz');
-        },
-        isValidRefName(refName, assemblyName) {
-            const { assemblyManager } = (0, util_1.getSession)(self);
-            return !assemblyName
-                ? false
-                : assemblyManager.isValidRefName(refName, assemblyName);
-        },
-        tracksForAssembly(selectedAssembly) {
-            const session = (0, util_1.getSession)(self);
-            const { tracks = [], sessionTracks = [] } = session;
-            const allTracks = [
-                ...tracks,
-                ...sessionTracks,
-            ];
-            return allTracks
-                .map(track => {
-                const assemblyNames = (0, configuration_1.readConfObject)(track, 'assemblyNames');
-                const adapter = (0, configuration_1.readConfObject)(track, 'adapter');
-                const category = (0, configuration_1.readConfObject)(track, 'category').join(',');
-                const loc = getAdapterLoc(adapter);
-                return assemblyNames.includes(selectedAssembly) && loc
-                    ? {
-                        track,
-                        label: [
-                            category ? `[${category}]` : '',
-                            (0, tracks_1.getTrackName)(track, session),
-                        ]
-                            .filter(f => !!f)
-                            .join(' '),
-                        assemblyNames,
-                        type: getType(adapter) || 'UNKNOWN',
-                        loc,
-                    }
-                    : undefined;
-            })
-                .filter(f => !!f)
-                .sort((a, b) => a.label.localeCompare(b.label));
-        },
-    }))
-        .actions(self => ({
-        setSelectedAssemblyName(s) {
-            self.selectedAssemblyName = s;
-        },
-        setFileSource(newSource) {
-            var _a;
-            self.fileSource = newSource;
-            self.error = undefined;
-            if (self.fileSource) {
-                const name = self.fileName;
-                if (name) {
-                    const firstMatch = (_a = fileTypesRegexp.exec(name)) === null || _a === void 0 ? void 0 : _a[1];
-                    if (firstMatch) {
-                        self.fileType =
-                            firstMatch === 'tsv' && name.includes('star-fusion')
-                                ? 'STAR-Fusion'
-                                : firstMatch.toUpperCase();
-                    }
-                }
-            }
-        },
-        setColumnNameLineNumber(newnumber) {
-            if (newnumber > 0) {
-                self.columnNameLineNumber = newnumber;
-            }
-        },
-        setFileType(typeName) {
-            self.fileType = typeName;
-        },
-        setError(error) {
-            self.error = error;
-        },
-        setLoading(arg) {
-            self.loading = arg;
-        },
-        cancelButton() {
-            self.error = undefined;
-            (0, mobx_state_tree_1.getParent)(self).setDisplayMode();
-        },
-        setCachedFileHandle(arg) {
-            self.cachedFileLocation = arg;
-        },
-    }))
-        .actions(self => ({
-        async import(assemblyName) {
-            if (!self.fileSource) {
-                return;
-            }
-            self.selectedAssemblyName = assemblyName;
-            const type = self.fileType;
-            const typeParser = await fileTypeParsers[type]();
-            const { fetchAndMaybeUnzip } = await Promise.resolve().then(() => __importStar(require('@jbrowse/core/util')));
-            const { pluginManager } = (0, util_1.getEnv)(self);
-            const filehandle = (0, io_1.openLocation)(self.fileSource, pluginManager);
-            self.setLoading(true);
-            try {
-                const stat = await filehandle.stat();
-                if (stat.size > IMPORT_SIZE_LIMIT) {
-                    self.setError(`File is too big. Tabular files are limited to at most ${(IMPORT_SIZE_LIMIT / 1000).toLocaleString()}kb.`);
-                    return;
-                }
-            }
-            catch (e) {
-                console.warn(e);
-            }
-            finally {
-                self.setLoading(false);
-            }
-            self.setLoading(true);
-            try {
-                if (self.fileSource.uri) {
-                    self.setCachedFileHandle({
-                        uri: self.fileSource.uri,
-                        baseUri: self.fileSource.baseUri,
-                        locationType: 'UriLocation',
-                    });
-                }
-                const data = await fetchAndMaybeUnzip(filehandle);
-                (0, mobx_state_tree_1.getParent)(self).displaySpreadsheet({
-                    ...typeParser(data),
-                    assemblyName,
-                });
-            }
-            catch (e) {
-                console.error(e);
-                self.setError(e);
-            }
-            finally {
-                self.setLoading(false);
-            }
-        },
-    }))
-        .actions(self => ({
-        afterAttach() {
-            ;
-            (async () => {
-                try {
-                    if (self.cachedFileLocation && self.selectedAssemblyName) {
-                        self.setFileSource(self.cachedFileLocation);
-                        await self.import(self.selectedAssemblyName);
-                    }
-                }
-                catch (e) {
-                    console.error(e);
-                    (0, util_1.getSession)(self).notifyError(`${e}`, e);
-                }
-            })();
-        },
-    }));
-}