@jbrowse/text-indexing 5.0.0-beta.1 → 5.0.0-beta.11

package/esm/TextIndexing.d.ts

@@ -1,14 +1,12 @@
 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: {
+import type { IndexingPolicy, Track } from '@jbrowse/text-indexing-core';
+export declare function indexTracks({ tracks, outDir, policy, assemblyNames, indexType, statusCallback, signal, }: {
     tracks: Track[];
     outDir: string;
-    stopToken?: StopToken;
-    attributesToIndex?: string[];
+    signal?: AbortSignal;
+    policy?: IndexingPolicy;
     assemblyNames?: string[];
-    featureTypesToExclude?: string[];
     indexType?: indexType;
     statusCallback: StatusCallback | undefined;
 }): Promise<void>;

package/esm/TextIndexing.js

@@ -1,89 +1,51 @@
-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 { 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 idxType = indexType || 'perTrack';
-    checkStopToken(stopToken);
-    await (idxType === 'perTrack'
-        ? perTrackIndex({
-            tracks,
-            statusCallback,
-            outDir,
-            attributesToIndex,
-            featureTypesToExclude,
-            stopToken,
-        })
-        : aggregateIndex({
-            tracks,
-            statusCallback,
-            outDir,
-            attributesToIndex,
-            assemblyNames,
-            featureTypesToExclude,
-            stopToken,
-        }));
-    checkStopToken(stopToken);
-}
-function ensureTrixDir(outDir) {
-    fs.mkdirSync(path.join(outDir, TRIX_DIR), { recursive: true });
-}
-async function perTrackIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, stopToken, }) {
-    ensureTrixDir(outDir);
-    const supportedTracks = tracks.filter(track => isSupportedIndexingAdapter(track.adapter?.type));
-    for (const trackConfig of supportedTracks) {
-        const { trackId, assemblyNames } = trackConfig;
-        await indexDriver({
-            tracks: [trackConfig],
-            outDir,
-            attributesToIndex,
-            name: `${trackId}-index`,
-            featureTypesToExclude,
-            assemblyNames,
-            statusCallback,
-            stopToken,
-        });
+import { checkAbortSignal } from '@jbrowse/core/util/aborting';
+import { defaultIndexingPolicy, isSupportedIndexingAdapter, writeTrixIndex, } from '@jbrowse/text-indexing-core';
+export async function indexTracks({ tracks, outDir, policy = defaultIndexingPolicy, assemblyNames, indexType = 'perTrack', statusCallback, signal, }) {
+    checkAbortSignal(signal);
+    const supported = tracks.filter(track => isSupportedIndexingAdapter(track.adapter?.type));
+    const write = (indexed, name, names) => indexDriver({
+        tracks: indexed,
+        outDir,
+        name,
+        policy,
+        assemblyNames: names,
+        statusCallback,
+        signal,
+    });
+    if (indexType === 'perTrack') {
+        for (const track of supported) {
+            await write([track], `${track.trackId}-index`, track.assemblyNames);
+        }
     }
-}
-async function aggregateIndex({ tracks, statusCallback, outDir, attributesToIndex = defaultAttributesToIndex, featureTypesToExclude = defaultFeatureTypesToExclude, stopToken, assemblyNames, }) {
-    if (!assemblyNames) {
-        throw new Error('No assemblies passed. Assemblies required for aggregate indexes');
+    else if (assemblyNames) {
+        for (const asm of assemblyNames) {
+            await write(supported.filter(track => track.assemblyNames.includes(asm)), `${asm}-index`, [asm]);
+        }
     }
-    ensureTrixDir(outDir);
-    for (const asm of assemblyNames) {
-        const supportedTracks = tracks
-            .filter(track => isSupportedIndexingAdapter(track.adapter?.type))
-            .filter(track => track.assemblyNames.includes(asm));
-        await indexDriver({
-            tracks: supportedTracks,
-            outDir,
-            attributesToIndex,
-            name: `${asm}-index`,
-            featureTypesToExclude,
-            assemblyNames: [asm],
-            statusCallback,
-            stopToken,
-        });
+    else {
+        throw new Error('No assemblies passed. Assemblies required for aggregate indexes');
     }
+    checkAbortSignal(signal);
 }
-async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, stopToken, }) {
-    const checker = createStopTokenChecker(stopToken);
+function indexDriver({ tracks, outDir, name, policy, 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
     // numerator only ever increases
     let bankedBytes = 0;
     let cumulativeTotal = 0;
-    const readable = Readable.from(indexFiles({
+    statusCallback?.('Indexing files');
+    return writeTrixIndex({
         tracks,
-        attributesToIndex,
         outDir,
-        featureTypesToExclude,
+        name,
+        policy,
+        assemblyNames,
         checkAbort: () => {
-            checkStopTokenThrottled(checker);
+            checkAbortSignal(signal);
+        },
+        onSort: () => {
+            statusCallback?.('Sorting and writing index');
         },
         makeProgress: () => {
             let trackTotal = 0;
@@ -104,26 +66,5 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
                 },
             };
         },
-    }));
-    // records stream straight into ixIxx, so 'end' is where the byte counts stop
-    // and the sort's own tail begins — otherwise minutes of a bar stuck at 100%
-    readable.on('end', () => {
-        statusCallback?.('Sorting and writing index');
     });
-    statusCallback?.('Indexing files');
-    await runIxIxx(readable, outDir, name);
-    checkStopToken(stopToken);
-    generateMeta({
-        configs: tracks,
-        attributesToIndex,
-        outDir,
-        name,
-        featureTypesToExclude,
-        assemblyNames,
-    });
-    checkStopToken(stopToken);
-}
-function runIxIxx(readStream, idxLocation, name) {
-    const { ix, ixx } = trixFilePaths(idxLocation, name);
-    return ixIxxStream(readStream, ix, ixx);
 }

package/esm/util.d.ts

@@ -1,8 +1,7 @@
 import type { Track } from '@jbrowse/text-indexing-core';
 export type indexType = 'aggregate' | 'perTrack';
-export declare function createTextSearchConf(name: string, trackIds: string[], assemblyNames: string[], locationPath: string): {
-    type: string;
-    textSearchAdapterId: string;
+export declare function createTextSearchConf(name: string, assemblyNames: string[], locationPath: string): {
+    type: 'TrixTextSearchAdapter';
     ixFilePath: {
         localPath: string;
         locationType: 'LocalPathLocation';
@@ -11,11 +10,6 @@ export declare function createTextSearchConf(name: string, trackIds: string[], a
         localPath: string;
         locationType: 'LocalPathLocation';
     };
-    metaFilePath: {
-        localPath: string;
-        locationType: 'LocalPathLocation';
-    };
-    tracks: string[];
     assemblyNames: string[];
 };
 export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[]): Track[];

package/esm/util.js

@@ -1,9 +1,8 @@
 import { isSupportedIndexingAdapter, trixFilePaths, } from '@jbrowse/text-indexing-core';
-export function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
+export function createTextSearchConf(name, assemblyNames, locationPath) {
     const paths = trixFilePaths(locationPath, name);
     return {
         type: 'TrixTextSearchAdapter',
-        textSearchAdapterId: name,
         ixFilePath: {
             localPath: paths.ix,
             locationType: 'LocalPathLocation',
@@ -12,11 +11,6 @@ export function createTextSearchConf(name, trackIds, assemblyNames, locationPath
             localPath: paths.ixx,
             locationType: 'LocalPathLocation',
         },
-        metaFilePath: {
-            localPath: paths.meta,
-            locationType: 'LocalPathLocation',
-        },
-        tracks: trackIds,
         assemblyNames,
     };
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "5.0.0-beta.1",
+  "version": "5.0.0-beta.11",
   "type": "module",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
@@ -20,13 +20,16 @@
   },
   "author": "JBrowse Team",
   "main": "esm/index.js",
+  "exports": {
+    ".": "./esm/index.js",
+    "./util": "./esm/util.js"
+  },
   "files": [
     "esm"
   ],
   "dependencies": {
-    "ixixx": "^3.0.13",
-    "@jbrowse/text-indexing-core": "^5.0.0-beta.1",
-    "@jbrowse/core": "^5.0.0-beta.1"
+    "@jbrowse/text-indexing-core": "^5.0.0-beta.11",
+    "@jbrowse/core": "^5.0.0-beta.11"
   },
   "peerDependencies": {
     "react": ">=19.0.0",
@@ -43,8 +46,5 @@
     "clean": "rimraf esm *.tsbuildinfo",
     "prebuild": "pnpm clean"
   },
-  "types": "esm/index.d.ts",
-  "exports": {
-    ".": "./esm/index.js"
-  }
+  "types": "esm/index.d.ts"
 }