@jbrowse/core 4.0.4 → 4.1.0

package/esm/util/jexl.js

@@ -24,6 +24,7 @@ export default function JexlF() {
     j.addFunction('charAt', (s, index) => s.charAt(index));
     j.addFunction('charCodeAt', (s, index) => s.charCodeAt(index));
     j.addFunction('codePointAt', (s, pos) => s.codePointAt(pos));
+    j.addFunction('includes', (s, search) => s.includes(search));
     j.addFunction('startsWith', (s, search, len) => s.startsWith(search, len));
     j.addFunction('endsWith', (s, search, len) => s.endsWith(search, len));
     j.addFunction('padEnd', (s, len, pad) => s.padEnd(len, pad));

package/esm/util/tracks.d.ts

@@ -1,4 +1,4 @@
-import type { FileLocation, PreFileLocation } from './types/index.ts';
+import type { BlobLocation, FileHandleLocation, FileLocation, PreFileLocation } from './types/index.ts';
 import type { AnyConfigurationModel } from '../configuration/index.ts';
 import type { IAnyStateTreeNode, IAnyType, Instance, types } from '@jbrowse/mobx-state-tree';
 export declare function getTrackAssemblyNames(track: IAnyStateTreeNode & {
@@ -12,12 +12,46 @@ export declare const UNSUPPORTED = "UNSUPPORTED";
 export declare function getBlob(id: string): File | undefined;
 export declare function getBlobMap(): Record<string, File>;
 export declare function setBlobMap(map: Record<string, File>): void;
-export declare function storeBlobLocation(location: PreFileLocation): import("./index.ts").PreUriLocation | import("./index.ts").PreLocalPathLocation | {
-    name: string;
-    blobId: string;
-    locationType: string;
-};
-export declare function makeIndex(location: FileLocation, suffix: string): import("./index.ts").BlobLocation | {
+export declare function storeBlobLocation(location: PreFileLocation): BlobLocation | PreFileLocation;
+export declare function getFileFromCache(handleId: string): File | undefined;
+export declare function setFileInCache(handleId: string, file: File): void;
+export declare function clearFileFromCache(handleId: string): void;
+export declare function getFileHandleCache(): Record<string, File>;
+export declare function setFileHandleCache(cache: Record<string, File>): void;
+export declare function ensureFileHandleReady(handleId: string, requestPermission?: boolean): Promise<File>;
+export declare function storeFileHandleLocation(handle: FileSystemFileHandle): Promise<FileHandleLocation>;
+export declare function restoreFileHandles(handleIds: string[], requestPermission?: boolean): Promise<({
+    handleId: string;
+    success: boolean;
+    error?: undefined;
+} | {
+    handleId: string;
+    success: boolean;
+    error: unknown;
+})[]>;
+export declare function findFileHandleIds(obj: unknown, handleIds?: Set<string>, seen?: WeakSet<object>): Set<string>;
+export declare function restoreFileHandlesFromSnapshot(sessionSnapshot: unknown, requestPermission?: boolean): Promise<({
+    handleId: string;
+    success: boolean;
+    error?: undefined;
+} | {
+    handleId: string;
+    success: boolean;
+    error: unknown;
+})[]>;
+export declare function getPendingFileHandleIds(): string[];
+export declare function setPendingFileHandleIds(ids: string[]): void;
+export declare function clearPendingFileHandleIds(): void;
+export declare function restorePendingFileHandles(): Promise<({
+    handleId: string;
+    success: boolean;
+    error?: undefined;
+} | {
+    handleId: string;
+    success: boolean;
+    error: unknown;
+})[]>;
+export declare function makeIndex(location: FileLocation, suffix: string): BlobLocation | FileHandleLocation | {
     uri: string;
     locationType: string;
     localPath?: undefined;

package/esm/util/tracks.js

@@ -1,4 +1,5 @@
-import { getParent, isRoot, isStateTreeNode } from '@jbrowse/mobx-state-tree';
+import { getParent, getSnapshot, isRoot, isStateTreeNode, } from '@jbrowse/mobx-state-tree';
+import { getFileHandle, storeFileHandle, verifyPermission, } from "./fileHandleStore.js";
 import { getEnv, getSession, objectHash } from "./index.js";
 import { readConfObject } from "../configuration/index.js";
 const trackAssemblyNamesCache = new WeakMap();
@@ -60,10 +61,121 @@ export function storeBlobLocation(location) {
     if ('blob' in location) {
         const blobId = `b${Date.now()}-${counter++}`;
         blobMap[blobId] = location.blob;
-        return { name: location.blob.name, blobId, locationType: 'BlobLocation' };
+        return {
+            name: location.blob.name,
+            blobId,
+            locationType: 'BlobLocation',
+        };
     }
     return location;
 }
+let fileHandleCache = {};
+export function getFileFromCache(handleId) {
+    return fileHandleCache[handleId];
+}
+export function setFileInCache(handleId, file) {
+    fileHandleCache[handleId] = file;
+}
+export function clearFileFromCache(handleId) {
+    delete fileHandleCache[handleId];
+}
+export function getFileHandleCache() {
+    return fileHandleCache;
+}
+export function setFileHandleCache(cache) {
+    fileHandleCache = cache;
+}
+export async function ensureFileHandleReady(handleId, requestPermission = true) {
+    const cached = fileHandleCache[handleId];
+    if (cached) {
+        return cached;
+    }
+    const handle = await getFileHandle(handleId);
+    if (!handle) {
+        throw new Error(`File handle not found for handleId: ${handleId}. The file may have been opened in a different browser or the IndexedDB was cleared.`);
+    }
+    const hasPermission = await verifyPermission(handle, requestPermission);
+    if (!hasPermission) {
+        throw new Error(`Permission denied for file "${handle.name}". Click "Restore access" to grant permission.`);
+    }
+    const file = await handle.getFile();
+    fileHandleCache[handleId] = file;
+    return file;
+}
+export async function storeFileHandleLocation(handle) {
+    const handleId = await storeFileHandle(handle);
+    const file = await handle.getFile();
+    fileHandleCache[handleId] = file;
+    return {
+        locationType: 'FileHandleLocation',
+        name: handle.name,
+        handleId,
+    };
+}
+export async function restoreFileHandles(handleIds, requestPermission = false) {
+    const results = [];
+    for (const handleId of handleIds) {
+        try {
+            await ensureFileHandleReady(handleId, requestPermission);
+            results.push({ handleId, success: true });
+        }
+        catch (e) {
+            results.push({ handleId, success: false, error: e });
+        }
+    }
+    return results;
+}
+export function findFileHandleIds(obj, handleIds = new Set(), seen = new WeakSet()) {
+    if (!obj || typeof obj !== 'object') {
+        return handleIds;
+    }
+    if (seen.has(obj)) {
+        return handleIds;
+    }
+    seen.add(obj);
+    if (Array.isArray(obj)) {
+        for (const item of obj) {
+            findFileHandleIds(item, handleIds, seen);
+        }
+    }
+    else {
+        const record = obj;
+        if (record.locationType === 'FileHandleLocation' &&
+            typeof record.handleId === 'string') {
+            handleIds.add(record.handleId);
+        }
+        for (const value of Object.values(record)) {
+            findFileHandleIds(value, handleIds, seen);
+        }
+    }
+    return handleIds;
+}
+export async function restoreFileHandlesFromSnapshot(sessionSnapshot, requestPermission = false) {
+    const handleIds = findFileHandleIds(sessionSnapshot);
+    if (handleIds.size > 0) {
+        return restoreFileHandles([...handleIds], requestPermission);
+    }
+    return [];
+}
+let pendingFileHandleIds = [];
+export function getPendingFileHandleIds() {
+    return pendingFileHandleIds;
+}
+export function setPendingFileHandleIds(ids) {
+    pendingFileHandleIds = ids;
+}
+export function clearPendingFileHandleIds() {
+    pendingFileHandleIds = [];
+}
+export async function restorePendingFileHandles() {
+    if (pendingFileHandleIds.length === 0) {
+        return [];
+    }
+    const results = await restoreFileHandles(pendingFileHandleIds, true);
+    const stillFailed = results.filter(r => !r.success).map(r => r.handleId);
+    pendingFileHandleIds = stillFailed;
+    return results;
+}
 export function makeIndex(location, suffix) {
     if ('uri' in location) {
         return {
@@ -88,10 +200,22 @@ export function getFileName(track) {
     const uri = 'uri' in track ? track.uri : undefined;
     const localPath = 'localPath' in track ? track.localPath : undefined;
     const blob = 'blobId' in track ? track : undefined;
-    return (blob?.name ||
-        uri?.slice(uri.lastIndexOf('/') + 1) ||
-        localPath?.slice(localPath.replace(/\\/g, '/').lastIndexOf('/') + 1) ||
-        '');
+    const fileHandle = 'handleId' in track ? track : undefined;
+    if (blob?.name) {
+        return blob.name;
+    }
+    if (fileHandle?.name) {
+        return fileHandle.name;
+    }
+    if (uri) {
+        const normalized = uri.replace(/\\/g, '/');
+        return normalized.slice(normalized.lastIndexOf('/') + 1);
+    }
+    if (localPath) {
+        const normalized = localPath.replace(/\\/g, '/');
+        return normalized.slice(normalized.lastIndexOf('/') + 1);
+    }
+    return '';
 }
 export function guessAdapter(file, index, adapterHint, model) {
     if (model) {
@@ -165,10 +289,14 @@ export function showTrackGeneric(self, trackId, initialSnapshot = {}, displayIni
     if (found) {
         return found;
     }
-    const conf = session.getTracksById()[trackId];
-    if (!conf) {
+    const rawConf = session.getTracksById()[trackId];
+    if (!rawConf) {
         throw new Error(`Could not resolve identifier "${trackId}"`);
     }
+    const confSnapshot = isStateTreeNode(rawConf)
+        ? getSnapshot(rawConf)
+        : structuredClone(rawConf);
+    const conf = pluginManager.evaluateExtensionPoint('Core-preProcessTrackConfig', confSnapshot);
     const trackType = pluginManager.getTrackType(conf.type);
     if (!trackType) {
         throw new Error(`Unknown track type ${conf.type}`);
@@ -177,12 +305,15 @@ export function showTrackGeneric(self, trackId, initialSnapshot = {}, displayIni
     const supportedDisplays = new Set(viewType.displayTypes.map(d => d.name));
     const displays = conf.displays ?? [];
     const displayConf = displays.find((d) => supportedDisplays.has(d.type));
-    const displayType = displayConf?.type ??
+    const snapshotType = displayInitialSnapshot.type;
+    const defaultDisplayType = displayConf?.type ??
         trackType.displayTypes.find(d => supportedDisplays.has(d.name))?.name;
+    const displayType = snapshotType ?? defaultDisplayType;
     if (!displayType) {
         throw new Error(`Could not find a compatible display for view type ${self.type}`);
     }
     const displayId = displayConf?.displayId ?? `${trackId}-${displayType}`;
+    const { type: _type, displayId: _displayId, ...displayConfState } = displayConf ?? {};
     const track = trackType.stateModel.create({
         ...initialSnapshot,
         type: conf.type,
@@ -191,6 +322,7 @@ export function showTrackGeneric(self, trackId, initialSnapshot = {}, displayIni
             {
                 type: displayType,
                 configuration: displayId,
+                ...displayConfState,
                 ...displayInitialSnapshot,
             },
         ],

package/esm/util/types/index.d.ts

@@ -1,5 +1,5 @@
 import type React from 'react';
-import type { BlobLocation as MUBlobLocation, LocalPathLocation as MULocalPathLocation, NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, UriLocation as MUUriLocation } from './mst.ts';
+import type { BlobLocation as MUBlobLocation, FileHandleLocation as MUFileHandleLocation, LocalPathLocation as MULocalPathLocation, NoAssemblyRegion as MUNoAssemblyRegion, Region as MUIRegion, UriLocation as MUUriLocation } from './mst.ts';
 import type TextSearchManager from '../../TextSearch/TextSearchManager.ts';
 import type assemblyManager from '../../assemblyManager/index.ts';
 import type { AnyConfigurationModel } from '../../configuration/index.ts';
@@ -64,7 +64,7 @@ export interface AbstractSessionModel extends AbstractViewContainer {
     clearSelection: () => void;
     duplicateCurrentSession?: () => void;
     notify: (message: string, level?: NotificationLevel, action?: SnackAction) => void;
-    notifyError: (message: string, error?: unknown, extra?: unknown) => void;
+    notifyError: (message: string, error?: unknown, extra?: unknown, action?: SnackAction) => void;
     assemblyManager: AssemblyManager;
     version: string;
     getTrackActionMenuItems?: (config: AnyConfigurationModel, extraTrackActions?: MenuItem[]) => MenuItem[];
@@ -246,6 +246,9 @@ export interface UriLocation extends SnapshotIn<typeof MUUriLocation> {
 export declare function isUriLocation(location: unknown): location is UriLocation;
 export declare function isLocalPathLocation(location: unknown): location is LocalPathLocation;
 export declare function isBlobLocation(location: unknown): location is BlobLocation;
+export interface FileHandleLocation extends SnapshotIn<typeof MUFileHandleLocation> {
+}
+export declare function isFileHandleLocation(location: unknown): location is FileHandleLocation;
 export declare class AuthNeededError extends Error {
     message: string;
     url: string;
@@ -260,7 +263,7 @@ export declare function isAuthNeededException(exception: unknown): exception is
 export declare function isRetryException(exception: Error): boolean;
 export interface BlobLocation extends SnapshotIn<typeof MUBlobLocation> {
 }
-export type FileLocation = LocalPathLocation | UriLocation | BlobLocation;
+export type FileLocation = LocalPathLocation | UriLocation | BlobLocation | FileHandleLocation;
 export interface PreUriLocation {
     uri: string;
 }
@@ -270,5 +273,8 @@ export interface PreLocalPathLocation {
 export interface PreBlobLocation {
     blob: File;
 }
-export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation;
+export interface PreFileHandleLocation {
+    handle: FileSystemFileHandle;
+}
+export type PreFileLocation = PreUriLocation | PreLocalPathLocation | PreBlobLocation | PreFileHandleLocation;
 export { default as TextSearchManager } from '../../TextSearch/TextSearchManager.ts';

package/esm/util/types/index.js

@@ -98,6 +98,12 @@ export function isBlobLocation(location) {
         'blobId' in location &&
         !!location.blobId);
 }
+export function isFileHandleLocation(location) {
+    return (typeof location === 'object' &&
+        location !== null &&
+        'handleId' in location &&
+        !!location.handleId);
+}
 export class AuthNeededError extends Error {
     message;
     url;

package/esm/util/types/mst.d.ts

@@ -25,6 +25,11 @@ export declare const BlobLocation: import("@jbrowse/mobx-state-tree").IModelType
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
 }, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
+export declare const FileHandleLocation: import("@jbrowse/mobx-state-tree").IModelType<{
+    locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+}, {}, import("@jbrowse/mobx-state-tree")._NotCustomized, import("@jbrowse/mobx-state-tree")._NotCustomized>;
 export declare const UriLocationRaw: import("@jbrowse/mobx-state-tree").IModelType<{
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"UriLocation">;
     uri: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -66,6 +71,10 @@ export declare const FileLocation: import("@jbrowse/mobx-state-tree").ISnapshotP
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+}>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
+    locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
 }>> | import("@jbrowse/mobx-state-tree").ModelCreationType<import("@jbrowse/mobx-state-tree/dist/internal").ExtractCFromProps<{
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -81,6 +90,10 @@ export declare const FileLocation: import("@jbrowse/mobx-state-tree").ISnapshotP
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+}> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
+    locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
 }> | import("@jbrowse/mobx-state-tree").ModelSnapshotType<{
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
@@ -88,6 +101,10 @@ export declare const FileLocation: import("@jbrowse/mobx-state-tree").ISnapshotP
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"BlobLocation">;
     name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
     blobId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+}, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
+    locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"FileHandleLocation">;
+    name: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
+    handleId: import("@jbrowse/mobx-state-tree").ISimpleType<string>;
 }, {}> | import("@jbrowse/mobx-state-tree").ModelInstanceType<{
     locationType: import("@jbrowse/mobx-state-tree").ISimpleType<"LocalPathLocation">;
     localPath: import("@jbrowse/mobx-state-tree").ISimpleType<string>;

package/esm/util/types/mst.js

@@ -23,6 +23,11 @@ export const BlobLocation = types.model('BlobLocation', {
     name: types.string,
     blobId: types.string,
 });
+export const FileHandleLocation = types.model('FileHandleLocation', {
+    locationType: types.literal('FileHandleLocation'),
+    name: types.string,
+    handleId: types.string,
+});
 export const UriLocationRaw = types.model('UriLocation', {
     locationType: types.literal('UriLocation'),
     uri: types.string,
@@ -42,14 +47,14 @@ export const UriLocation = types.snapshotProcessor(UriLocationRaw, {
         return snap;
     },
 });
-export const FileLocation = types.snapshotProcessor(types.union(LocalPathLocation, UriLocation, BlobLocation), {
+export const FileLocation = types.snapshotProcessor(types.union(LocalPathLocation, UriLocation, BlobLocation, FileHandleLocation), {
     preProcessor(snap) {
         if (!snap) {
             return undefined;
         }
         const { locationType, ...rest } = snap;
         if (!locationType) {
-            const { uri, localPath, blob } = rest;
+            const { uri, localPath, blob, handleId } = rest;
             let locationType = '';
             if (uri !== undefined) {
                 locationType = 'UriLocation';
@@ -60,6 +65,9 @@ export const FileLocation = types.snapshotProcessor(types.union(LocalPathLocatio
             else if (blob !== undefined) {
                 locationType = 'BlobLocation';
             }
+            else if (handleId !== undefined) {
+                locationType = 'FileHandleLocation';
+            }
             return { ...rest, locationType };
         }
         return snap;