@jbrowse/plugin-spreadsheet-view 3.7.0 → 4.0.1

package/esm/LaunchSpreadsheetView/index.js

@@ -1,18 +1,11 @@
 export default 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',
+        session.addView('SpreadsheetView', {
+            init: {
+                assembly,
+                uri,
+                fileType,
+            },
         });
-        await view.importWizard.import(assembly);
     });
 }

package/esm/SpreadsheetView/ImportWizard.d.ts

@@ -1,11 +1,11 @@
 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>;
+import type { Instance } from '@jbrowse/mobx-state-tree';
+export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+    fileType: import("@jbrowse/mobx-state-tree").IOptionalIType<import("@jbrowse/mobx-state-tree").ISimpleType<string>, [undefined]>;
+    hasColumnNameLine: import("@jbrowse/mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
+    columnNameLineNumber: import("@jbrowse/mobx-state-tree").IType<number | undefined, number, number>;
+    selectedAssemblyName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    cachedFileLocation: import("@jbrowse/mobx-state-tree").IType<FileLocation | undefined, FileLocation | undefined, FileLocation | undefined>;
 }, {
     fileTypes: string[];
     fileSource: any;
@@ -19,15 +19,11 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     tracksForAssembly(selectedAssembly: string): {
         track: {
             [x: string]: any;
-        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        } & import("@jbrowse/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>;
+            } & import("@jbrowse/mobx-state-tree/dist/internal").NonEmptyObject & any & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
+        } & import("@jbrowse/mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>;
         label: string;
         assemblyNames: any;
         type: string;
@@ -46,6 +42,6 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     import(assemblyName: string): Promise<void>;
 } & {
     afterAttach(): void;
-}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;
+}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type ImportWizardStateModel = ReturnType<typeof stateModelFactory>;
 export type ImportWizardModel = Instance<ImportWizardStateModel>;

package/esm/SpreadsheetView/ImportWizard.js

@@ -2,35 +2,30 @@ import { readConfObject } from '@jbrowse/core/configuration';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import { openLocation } from '@jbrowse/core/util/io';
 import { getTrackName } from '@jbrowse/core/util/tracks';
-import { getParent, types } from 'mobx-state-tree';
-const IMPORT_SIZE_LIMIT = 100000000;
+import { getParent, types } from '@jbrowse/mobx-state-tree';
+const IMPORT_SIZE_LIMIT = 100_000_000;
 const fileTypes = ['VCF', 'BED', 'BEDPE', 'STAR-Fusion'];
 const fileTypeParsers = {
-    VCF: () => import('./importAdapters/VcfImport').then(r => r.parseVcfBuffer),
-    BED: () => import('./importAdapters/BedImport').then(r => r.parseBedBuffer),
-    BEDPE: () => import('./importAdapters/BedpeImport').then(r => r.parseBedPEBuffer),
-    'STAR-Fusion': () => import('./importAdapters/STARFusionImport').then(r => r.parseSTARFusionBuffer),
+    VCF: () => import("./importAdapters/VcfImport.js").then(r => r.parseVcfBuffer),
+    BED: () => import("./importAdapters/BedImport.js").then(r => r.parseBedBuffer),
+    BEDPE: () => import("./importAdapters/BedpeImport.js").then(r => r.parseBedPEBuffer),
+    'STAR-Fusion': () => import("./importAdapters/STARFusionImport.js").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 {
+const adapterTypeMap = {
+    VcfAdapter: { fileType: 'VCF', locationKey: 'vcfLocation' },
+    VcfTabixAdapter: { fileType: 'VCF', locationKey: 'vcfGzLocation' },
+    BedAdapter: { fileType: 'BED', locationKey: 'bedLocation' },
+    BedTabixAdapter: { fileType: 'BED', locationKey: 'bedGzLocation' },
+    BedpeAdapter: { fileType: 'BEDPE', locationKey: 'bedpeLocation' },
+};
+function getAdapterInfo(adapter) {
+    const entry = adapterTypeMap[adapter.type];
+    if (!entry) {
         return undefined;
     }
-}
-function getAdapterLoc(adapter) {
-    return (adapter.vcfLocation ||
-        adapter.vcfGzLocation ||
-        adapter.bedLocation ||
-        adapter.bedGzLocation ||
-        adapter.bedpeLocation);
+    const loc = adapter[entry.locationKey] ??
+        adapter;
+    return { fileType: entry.fileType, loc };
 }
 const fileTypesRegexp = new RegExp(String.raw `\.(${fileTypes.join('|')})(\.gz)?$`, 'i');
 function x() { }
@@ -72,33 +67,37 @@ export default function stateModelFactory() {
         },
         tracksForAssembly(selectedAssembly) {
             const session = getSession(self);
-            const { tracks = [], sessionTracks = [] } = session;
+            const { tracks, sessionTracks = [] } = session;
             const allTracks = [
                 ...tracks,
                 ...sessionTracks,
             ];
             return allTracks
-                .map(track => {
-                const assemblyNames = readConfObject(track, 'assemblyNames');
+                .flatMap(track => {
+                const assemblyNames = readConfObject(track, 'assemblyNames') ?? [];
+                if (!assemblyNames.includes(selectedAssembly)) {
+                    return [];
+                }
                 const adapter = readConfObject(track, 'adapter');
-                const category = readConfObject(track, 'category').join(',');
-                const loc = getAdapterLoc(adapter);
-                return assemblyNames.includes(selectedAssembly) && loc
-                    ? {
-                        track,
-                        label: [
-                            category ? `[${category}]` : '',
-                            getTrackName(track, session),
-                        ]
-                            .filter(f => !!f)
-                            .join(' '),
-                        assemblyNames,
-                        type: getType(adapter) || 'UNKNOWN',
-                        loc,
-                    }
-                    : undefined;
+                const info = getAdapterInfo(adapter);
+                if (!info) {
+                    return [];
+                }
+                const category = readConfObject(track, 'category') ?? [];
+                const categoryStr = category.join(',');
+                return {
+                    track,
+                    label: [
+                        categoryStr ? `[${categoryStr}]` : '',
+                        getTrackName(track, session),
+                    ]
+                        .filter(f => !!f)
+                        .join(' '),
+                    assemblyNames,
+                    type: info.fileType,
+                    loc: info.loc,
+                };
             })
-                .filter(f => !!f)
                 .sort((a, b) => a.label.localeCompare(b.label));
         },
     }))
@@ -107,13 +106,12 @@ export default function stateModelFactory() {
             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];
+                    const firstMatch = fileTypesRegexp.exec(name)?.[1];
                     if (firstMatch) {
                         self.fileType =
                             firstMatch === 'tsv' && name.includes('star-fusion')

package/esm/SpreadsheetView/SpreadsheetModel.d.ts

@@ -1,5 +1,5 @@
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import type { Instance } from 'mobx-state-tree';
+import type { Instance } from '@jbrowse/mobx-state-tree';
 export interface Row {
     feature?: SimpleFeatureSerialized;
     cellData?: Record<string, unknown>;
@@ -10,17 +10,17 @@ export interface Row {
 export interface RowSet {
     rows: Row[];
 }
-export default function stateModelFactory(): import("mobx-state-tree").IModelType<{
-    rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
-    columns: import("mobx-state-tree").IType<{
+export default function stateModelFactory(): import("@jbrowse/mobx-state-tree").IModelType<{
+    rowSet: import("@jbrowse/mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
+    columns: import("@jbrowse/mobx-state-tree").IType<{
         name: string;
     }[], {
         name: string;
     }[], {
         name: string;
     }[]>;
-    assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
+    assemblyName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    visibleColumns: import("@jbrowse/mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
 }, {
     visibleRowFlags: Record<number, boolean> | undefined;
 } & {
@@ -37,10 +37,7 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
     } | {
         field: string;
         width: number;
-        renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<{
-            id: number;
-            feature: SimpleFeatureSerialized | undefined;
-        }, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
+        renderCell: ({ row }: import("@mui/x-data-grid").GridRenderCellParams<any, any, any, import("@mui/x-data-grid").GridTreeNodeWithRender>) => import("react/jsx-runtime").JSX.Element | "N/A";
         type?: undefined;
         valueGetter?: undefined;
         valueFormatter?: undefined;
@@ -62,17 +59,17 @@ export default function stateModelFactory(): import("mobx-state-tree").IModelTyp
 } & {
     setVisibleRows(arg?: Record<number, boolean>): void;
     setVisibleColumns(arg: Record<string, boolean>): void;
-}, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
-    rowSet: import("mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
-    columns: import("mobx-state-tree").IType<{
+}, import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+    rowSet: import("@jbrowse/mobx-state-tree").IType<RowSet | undefined, RowSet | undefined, RowSet | undefined>;
+    columns: import("@jbrowse/mobx-state-tree").IType<{
         name: string;
     }[], {
         name: string;
     }[], {
         name: string;
     }[]>;
-    assemblyName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
-    visibleColumns: import("mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
-}>>, import("mobx-state-tree")._NotCustomized>;
+    assemblyName: import("@jbrowse/mobx-state-tree").IMaybe<import("@jbrowse/mobx-state-tree").ISimpleType<string>>;
+    visibleColumns: import("@jbrowse/mobx-state-tree").IType<Record<string, boolean>, Record<string, boolean>, Record<string, boolean>>;
+}>>, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export type SpreadsheetStateModel = ReturnType<typeof stateModelFactory>;
 export type SpreadsheetModel = Instance<SpreadsheetStateModel>;

package/esm/SpreadsheetView/SpreadsheetModel.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { assembleLocStringFast, getSession, measureGridWidth, toLocale, } from '@jbrowse/core/util';
-import { types } from 'mobx-state-tree';
-import LocationCell from './components/LocationCell';
+import { types } from '@jbrowse/mobx-state-tree';
+import LocationCell from "./components/LocationCell.js";
 export default function stateModelFactory() {
     return types
         .model('Spreadsheet', {
@@ -15,25 +15,20 @@ export default function stateModelFactory() {
     }))
         .views(self => ({
         get rows() {
-            var _a;
-            return (_a = self.rowSet) === null || _a === void 0 ? void 0 : _a.rows.map((row, i) => ({
+            return self.rowSet?.rows.map((row, i) => ({
                 id: i,
                 feature: row.feature,
-                ...Object.fromEntries(self.columns.map((c, idx) => {
-                    var _a, _b, _c, _d;
-                    return [
-                        c.name,
-                        (_b = (_a = row.cellData) === null || _a === void 0 ? void 0 : _a[c.name]) !== null && _b !== void 0 ? _b : (_d = (_c = row.cells) === null || _c === void 0 ? void 0 : _c[idx]) === null || _d === void 0 ? void 0 : _d.text,
-                    ];
-                })),
+                ...Object.fromEntries(self.columns.map((c, idx) => [
+                    c.name,
+                    row.cellData?.[c.name] ?? row.cells?.[idx]?.text,
+                ])),
             }));
         },
         get initialized() {
-            var _a;
             const session = getSession(self);
             const name = self.assemblyName;
             return (self.rowSet &&
-                (name ? (_a = session.assemblyManager.get(name)) === null || _a === void 0 ? void 0 : _a.initialized : false));
+                (name ? session.assemblyManager.get(name)?.initialized : false));
         },
     }))
         .views(self => ({
@@ -75,10 +70,9 @@ export default function stateModelFactory() {
     }))
         .views(self => ({
         get visibleRows() {
-            var _a;
             const { visibleRowFlags } = self;
             return visibleRowFlags
-                ? (_a = self.rows) === null || _a === void 0 ? void 0 : _a.filter((_f, idx) => visibleRowFlags[idx] !== false)
+                ? self.rows?.filter((_f, idx) => visibleRowFlags[idx] !== false)
                 : self.rows;
         },
     }))
@@ -98,13 +92,11 @@ export default function stateModelFactory() {
                 rowSet: snap.rowSet
                     ? {
                         ...snap.rowSet,
-                        rows: snap.rowSet.rows.map(r => {
-                            var _a, _b;
-                            return ({
-                                ...r,
-                                feature: (_a = r.feature) !== null && _a !== void 0 ? _a : (_b = r.extendedData) === null || _b === void 0 ? void 0 : _b.vcfFeature,
-                            });
-                        }),
+                        rows: snap.rowSet.rows.map(r => ({
+                            ...r,
+                            feature: r.feature ??
+                                r.extendedData?.vcfFeature,
+                        })),
                     }
                     : undefined,
             }