@jbrowse/text-indexing 5.0.0-beta.8 → 5.0.0-beta.9

package/esm/TextIndexing.d.ts

@@ -1,11 +1,10 @@
 import type { indexType } from './util.ts';
 import type { StatusCallback } from '@jbrowse/core/util';
-import type { StopToken } from '@jbrowse/core/util/stopToken';
 import type { Track } from '@jbrowse/text-indexing-core';
 export declare function indexTracks(args: {
     tracks: Track[];
     outDir: string;
-    stopToken?: StopToken;
+    signal?: AbortSignal;
     attributesToIndex?: string[];
     assemblyNames?: string[];
     featureTypesToExclude?: string[];

package/esm/TextIndexing.js

@@ -1,13 +1,13 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import { Readable } from 'node:stream';
-import { checkStopTokenThrottled, checkStopToken, createStopTokenChecker, } from '@jbrowse/core/util/stopToken';
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
 import { TRIX_DIR, defaultAttributesToIndex, defaultFeatureTypesToExclude, generateMeta, indexFiles, isSupportedIndexingAdapter, trixFilePaths, } from '@jbrowse/text-indexing-core';
 import { ixIxxStream } from 'ixixx';
 export async function indexTracks(args) {
-    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, stopToken, } = args;
+    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, signal, } = args;
     const idxType = indexType || 'perTrack';
-    checkStopToken(stopToken);
+    checkAbortSignal(signal);
     await (idxType === 'perTrack'
         ? perTrackIndex({
             tracks,
@@ -15,7 +15,7 @@ export async function indexTracks(args) {
             outDir,
             attributesToIndex,
             featureTypesToExclude,
-            stopToken,
+            signal,
         })
         : aggregateIndex({
             tracks,
@@ -24,14 +24,14 @@ export async function indexTracks(args) {
             attributesToIndex,
             assemblyNames,
             featureTypesToExclude,
-            stopToken,
+            signal,
         }));
-    checkStopToken(stopToken);
+    checkAbortSignal(signal);
 }
 function ensureTrixDir(outDir) {
     fs.mkdirSync(path.join(outDir, TRIX_DIR), { recursive: true });
 }
-async function perTrackIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, stopToken, }) {
+async function perTrackIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, signal, }) {
     ensureTrixDir(outDir);
     const supportedTracks = tracks.filter(track => isSupportedIndexingAdapter(track.adapter?.type));
     for (const trackConfig of supportedTracks) {
@@ -44,11 +44,11 @@ async function perTrackIndex({ tracks, statusCallback, outDir, attributesToIndex
             featureTypesToExclude,
             assemblyNames,
             statusCallback,
-            stopToken,
+            signal,
         });
     }
 }
-async function aggregateIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, stopToken, assemblyNames, }) {
+async function aggregateIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, signal, assemblyNames, }) {
     if (!assemblyNames) {
         throw new Error('No assemblies passed. Assemblies required for aggregate indexes');
     }
@@ -65,12 +65,11 @@ async function aggregateIndex({ tracks, statusCallback, outDir, attributesToInde
             featureTypesToExclude,
             assemblyNames: [asm],
             statusCallback,
-            stopToken,
+            signal,
         });
     }
 }
-async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, stopToken, }) {
-    const checker = createStopTokenChecker(stopToken);
+async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, signal, }) {
     // accumulate across tracks so an aggregate index reports monotonic progress
     // rather than resetting to zero at each track. The denominator grows as each
     // track's size is discovered (we don't stat every file up front), but the
@@ -83,7 +82,7 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
         outDir,
         featureTypesToExclude,
         checkAbort: () => {
-            checkStopTokenThrottled(checker);
+            checkAbortSignal(signal);
         },
         makeProgress: () => {
             let trackTotal = 0;
@@ -112,7 +111,7 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
     });
     statusCallback?.('Indexing files');
     await runIxIxx(readable, outDir, name);
-    checkStopToken(stopToken);
+    checkAbortSignal(signal);
     generateMeta({
         configs: tracks,
         attributesToIndex,
@@ -121,7 +120,7 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
         featureTypesToExclude,
         assemblyNames,
     });
-    checkStopToken(stopToken);
+    checkAbortSignal(signal);
 }
 function runIxIxx(readStream, idxLocation, name) {
     const { ix, ixx } = trixFilePaths(idxLocation, name);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "5.0.0-beta.8",
+  "version": "5.0.0-beta.9",
   "type": "module",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
@@ -29,8 +29,8 @@
   ],
   "dependencies": {
     "ixixx": "^3.0.13",
-    "@jbrowse/text-indexing-core": "^5.0.0-beta.8",
-    "@jbrowse/core": "^5.0.0-beta.8"
+    "@jbrowse/core": "^5.0.0-beta.9",
+    "@jbrowse/text-indexing-core": "^5.0.0-beta.9"
   },
   "peerDependencies": {
     "react": ">=19.0.0",