@jbrowse/text-indexing 2.17.0 → 3.0.0

package/dist/TextIndexing.d.ts

@@ -1,8 +1,8 @@
-import { Track, indexType } from './util';
+import type { Track, indexType } from './util';
 export declare function indexTracks(args: {
     tracks: Track[];
     outDir?: string;
-    signal?: AbortSignal;
+    stopToken?: string;
     attributesToIndex?: string[];
     assemblyNames?: string[];
     featureTypesToExclude?: string[];

package/dist/TextIndexing.js

@@ -7,15 +7,16 @@ exports.indexTracks = indexTracks;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const stream_1 = require("stream");
+const util_1 = require("@jbrowse/core/util");
+const stopToken_1 = require("@jbrowse/core/util/stopToken");
+const ixixx_1 = require("ixixx");
+const common_1 = require("./types/common");
 const gff3Adapter_1 = require("./types/gff3Adapter");
 const vcfAdapter_1 = require("./types/vcfAdapter");
-const common_1 = require("./types/common");
-const ixixx_1 = require("ixixx");
-const util_1 = require("@jbrowse/core/util");
 async function indexTracks(args) {
-    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, signal, } = args;
+    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, stopToken, } = args;
     const idxType = indexType || 'perTrack';
-    (0, util_1.checkAbortSignal)(signal);
+    (0, stopToken_1.checkStopToken)(stopToken);
     await (idxType === 'perTrack'
         ? perTrackIndex({
             tracks,
@@ -23,7 +24,7 @@ async function indexTracks(args) {
             outDir,
             attributesToIndex,
             featureTypesToExclude,
-            signal,
+            stopToken,
         })
         : aggregateIndex({
             tracks,
@@ -32,12 +33,12 @@ async function indexTracks(args) {
             attributesToIndex,
             assemblyNames,
             featureTypesToExclude,
-            signal,
+            stopToken,
         }));
-    (0, util_1.checkAbortSignal)(signal);
+    (0, stopToken_1.checkStopToken)(stopToken);
     return [];
 }
-async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, }) {
+async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, }) {
     const outFlag = paramOutDir || '.';
     const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
@@ -46,7 +47,6 @@ async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attr
     if (!fs_1.default.existsSync(trixDir)) {
         fs_1.default.mkdirSync(trixDir);
     }
-    // default settings
     const supportedTracks = tracks.filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
     for (const trackConfig of supportedTracks) {
         const { trackId, assemblyNames } = trackConfig;
@@ -59,11 +59,11 @@ async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attr
             featureTypesToExclude,
             assemblyNames,
             statusCallback,
-            signal,
+            stopToken,
         });
     }
 }
-async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, assemblyNames, }) {
+async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, assemblyNames, }) {
     const outFlag = paramOutDir || '.';
     const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
@@ -88,22 +88,22 @@ async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, att
             featureTypesToExclude,
             assemblyNames: [asm],
             statusCallback,
-            signal,
+            stopToken,
         });
     }
 }
-async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, signal, }) {
+async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, stopToken, }) {
     const readable = stream_1.Readable.from(indexFiles({
         tracks,
         attributesToIndex,
         outDir,
         featureTypesToExclude,
         statusCallback,
-        signal,
+        stopToken,
     }));
     statusCallback('Indexing files.');
     await runIxIxx(readable, outDir, name);
-    (0, util_1.checkAbortSignal)(signal);
+    (0, stopToken_1.checkStopToken)(stopToken);
     await (0, common_1.generateMeta)({
         configs: tracks,
         attributesToIndex,
@@ -112,7 +112,7 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
         featureTypesToExclude,
         assemblyNames,
     });
-    (0, util_1.checkAbortSignal)(signal);
+    (0, stopToken_1.checkStopToken)(stopToken);
 }
 async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTypesToExclude: edx1, statusCallback, }) {
     for (const track of tracks) {

package/dist/types/common.d.ts

@@ -1,6 +1,6 @@
 import fs from 'fs';
 import fetch from 'node-fetch';
-import { LocalPathLocation, UriLocation, Track } from '../util';
+import type { LocalPathLocation, Track, UriLocation } from '../util';
 export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
 export declare function isURL(FileName: string): boolean;
 export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {
@@ -11,9 +11,6 @@ export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onT
 }): Promise<NodeJS.ReadableStream | fs.ReadStream>;
 export declare function makeLocation(location: string, protocol: string): UriLocation | LocalPathLocation;
 export declare function guessAdapterFromFileName(filePath: string): Track;
-/**
- * Generates metadata of index given a filename (trackId or assembly)
- */
 export declare function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }: {
     configs: Track[];
     attributesToIndex: string[];

package/dist/types/common.js

@@ -10,10 +10,8 @@ exports.makeLocation = makeLocation;
 exports.guessAdapterFromFileName = guessAdapterFromFileName;
 exports.generateMeta = generateMeta;
 const fs_1 = __importDefault(require("fs"));
-const node_fetch_1 = __importDefault(require("node-fetch"));
 const path_1 = __importDefault(require("path"));
-// Method for handing off the parsing of a gff3 file URL. Calls the proper
-// parser depending on if it is gzipped or not. Returns a @gmod/gff stream.
+const node_fetch_1 = __importDefault(require("node-fetch"));
 async function createRemoteStream(urlIn) {
     const res = await (0, node_fetch_1.default)(urlIn);
     if (!res.ok) {
@@ -21,8 +19,6 @@ async function createRemoteStream(urlIn) {
     }
     return res;
 }
-// Checks if the passed in string is a valid URL.
-// Returns a boolean.
 function isURL(FileName) {
     let url;
     try {
@@ -68,7 +64,6 @@ function makeLocation(location, protocol) {
     throw new Error(`invalid protocol ${protocol}`);
 }
 function guessAdapterFromFileName(filePath) {
-    // const uri = isURL(filePath) ? filePath : path.resolve(filePath)
     const protocol = isURL(filePath) ? 'uri' : 'localPath';
     const name = path_1.default.basename(filePath);
     if (/\.vcf\.b?gz$/i.test(filePath)) {
@@ -130,9 +125,6 @@ function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
-/**
- * Generates metadata of index given a filename (trackId or assembly)
- */
 async function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }) {
     fs_1.default.writeFileSync(path_1.default.join(outDir, 'trix', `${name}_meta.json`), JSON.stringify({
         dateCreated: new Date().toISOString(),

package/dist/types/gff3Adapter.js

@@ -4,9 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexGff3 = indexGff3;
-const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
-// locals
+const zlib_1 = require("zlib");
 const util_1 = require("../util");
 const common_1 = require("./common");
 async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
@@ -33,8 +32,6 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featu
         const [seq_id, , type, start, end, , , , col9] = line.split('\t');
         const locStr = `${seq_id}:${start}..${end}`;
         if (!featureTypesToExclude.includes(type)) {
-            // turns gff3 attrs into a map, and converts the arrays into space
-            // separated strings
             const col9attrs = Object.fromEntries(col9
                 .split(';')
                 .map(f => f.trim())

package/dist/types/vcfAdapter.js

@@ -4,9 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexVcf = indexVcf;
-const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
-// locals
+const zlib_1 = require("zlib");
 const util_1 = require("../util");
 const common_1 = require("./common");
 async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
@@ -27,10 +26,7 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStar
         if (line.startsWith('#')) {
             continue;
         }
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
         const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        // turns gff3 attrs into a map, and converts the arrays into space
-        // separated strings
         const fields = Object.fromEntries(info
             .split(';')
             .map(f => f.trim())

package/dist/util.js

@@ -6,9 +6,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.createTextSearchConf = createTextSearchConf;
 exports.findTrackConfigsToIndex = findTrackConfigsToIndex;
 exports.decodeURIComponentNoThrow = decodeURIComponentNoThrow;
+const path_1 = __importDefault(require("path"));
 const util_1 = require("@jbrowse/core/util");
 const sanitize_filename_1 = __importDefault(require("sanitize-filename"));
-const path_1 = __importDefault(require("path"));
 function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
     const base = path_1.default.join(locationPath, 'trix');
     const n = (0, sanitize_filename_1.default)(name);
@@ -48,7 +48,6 @@ function decodeURIComponentNoThrow(uri) {
         return decodeURIComponent(uri);
     }
     catch (e) {
-        // avoid throwing exception on a failure to decode URI component
         return uri;
     }
 }

package/esm/TextIndexing.d.ts

@@ -1,8 +1,8 @@
-import { Track, indexType } from './util';
+import type { Track, indexType } from './util';
 export declare function indexTracks(args: {
     tracks: Track[];
     outDir?: string;
-    signal?: AbortSignal;
+    stopToken?: string;
     attributesToIndex?: string[];
     assemblyNames?: string[];
     featureTypesToExclude?: string[];

package/esm/TextIndexing.js

@@ -1,15 +1,16 @@
 import fs from 'fs';
 import path from 'path';
 import { Readable } from 'stream';
+import { isSupportedIndexingAdapter } from '@jbrowse/core/util';
+import { checkStopToken } from '@jbrowse/core/util/stopToken';
+import { ixIxxStream } from 'ixixx';
+import { generateMeta } from './types/common';
 import { indexGff3 } from './types/gff3Adapter';
 import { indexVcf } from './types/vcfAdapter';
-import { generateMeta } from './types/common';
-import { ixIxxStream } from 'ixixx';
-import { checkAbortSignal, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
 export async function indexTracks(args) {
-    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, signal, } = args;
+    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, stopToken, } = args;
     const idxType = indexType || 'perTrack';
-    checkAbortSignal(signal);
+    checkStopToken(stopToken);
     await (idxType === 'perTrack'
         ? perTrackIndex({
             tracks,
@@ -17,7 +18,7 @@ export async function indexTracks(args) {
             outDir,
             attributesToIndex,
             featureTypesToExclude,
-            signal,
+            stopToken,
         })
         : aggregateIndex({
             tracks,
@@ -26,12 +27,12 @@ export async function indexTracks(args) {
             attributesToIndex,
             assemblyNames,
             featureTypesToExclude,
-            signal,
+            stopToken,
         }));
-    checkAbortSignal(signal);
+    checkStopToken(stopToken);
     return [];
 }
-async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, }) {
+async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, }) {
     const outFlag = paramOutDir || '.';
     const isDir = fs.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path.join(outFlag, 'config.json') : outFlag;
@@ -40,7 +41,6 @@ async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attr
     if (!fs.existsSync(trixDir)) {
         fs.mkdirSync(trixDir);
     }
-    // default settings
     const supportedTracks = tracks.filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
     for (const trackConfig of supportedTracks) {
         const { trackId, assemblyNames } = trackConfig;
@@ -53,11 +53,11 @@ async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attr
             featureTypesToExclude,
             assemblyNames,
             statusCallback,
-            signal,
+            stopToken,
         });
     }
 }
-async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, assemblyNames, }) {
+async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], stopToken, assemblyNames, }) {
     const outFlag = paramOutDir || '.';
     const isDir = fs.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path.join(outFlag, 'config.json') : outFlag;
@@ -82,22 +82,22 @@ async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, att
             featureTypesToExclude,
             assemblyNames: [asm],
             statusCallback,
-            signal,
+            stopToken,
         });
     }
 }
-async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, signal, }) {
+async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, stopToken, }) {
     const readable = Readable.from(indexFiles({
         tracks,
         attributesToIndex,
         outDir,
         featureTypesToExclude,
         statusCallback,
-        signal,
+        stopToken,
     }));
     statusCallback('Indexing files.');
     await runIxIxx(readable, outDir, name);
-    checkAbortSignal(signal);
+    checkStopToken(stopToken);
     await generateMeta({
         configs: tracks,
         attributesToIndex,
@@ -106,7 +106,7 @@ async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTyp
         featureTypesToExclude,
         assemblyNames,
     });
-    checkAbortSignal(signal);
+    checkStopToken(stopToken);
 }
 async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTypesToExclude: edx1, statusCallback, }) {
     for (const track of tracks) {

package/esm/types/common.d.ts

@@ -1,6 +1,6 @@
 import fs from 'fs';
 import fetch from 'node-fetch';
-import { LocalPathLocation, UriLocation, Track } from '../util';
+import type { LocalPathLocation, Track, UriLocation } from '../util';
 export declare function createRemoteStream(urlIn: string): Promise<fetch.Response>;
 export declare function isURL(FileName: string): boolean;
 export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onTotalBytes, }: {
@@ -11,9 +11,6 @@ export declare function getLocalOrRemoteStream({ file, out, onBytesReceived, onT
 }): Promise<NodeJS.ReadableStream | fs.ReadStream>;
 export declare function makeLocation(location: string, protocol: string): UriLocation | LocalPathLocation;
 export declare function guessAdapterFromFileName(filePath: string): Track;
-/**
- * Generates metadata of index given a filename (trackId or assembly)
- */
 export declare function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }: {
     configs: Track[];
     attributesToIndex: string[];

package/esm/types/common.js

@@ -1,8 +1,6 @@
 import fs from 'fs';
-import fetch from 'node-fetch';
 import path from 'path';
-// Method for handing off the parsing of a gff3 file URL. Calls the proper
-// parser depending on if it is gzipped or not. Returns a @gmod/gff stream.
+import fetch from 'node-fetch';
 export async function createRemoteStream(urlIn) {
     const res = await fetch(urlIn);
     if (!res.ok) {
@@ -10,8 +8,6 @@ export async function createRemoteStream(urlIn) {
     }
     return res;
 }
-// Checks if the passed in string is a valid URL.
-// Returns a boolean.
 export function isURL(FileName) {
     let url;
     try {
@@ -57,7 +53,6 @@ export function makeLocation(location, protocol) {
     throw new Error(`invalid protocol ${protocol}`);
 }
 export function guessAdapterFromFileName(filePath) {
-    // const uri = isURL(filePath) ? filePath : path.resolve(filePath)
     const protocol = isURL(filePath) ? 'uri' : 'localPath';
     const name = path.basename(filePath);
     if (/\.vcf\.b?gz$/i.test(filePath)) {
@@ -119,9 +114,6 @@ export function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
-/**
- * Generates metadata of index given a filename (trackId or assembly)
- */
 export async function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }) {
     fs.writeFileSync(path.join(outDir, 'trix', `${name}_meta.json`), JSON.stringify({
         dateCreated: new Date().toISOString(),

package/esm/types/gff3Adapter.js

@@ -1,6 +1,5 @@
-import { createGunzip } from 'zlib';
 import readline from 'readline';
-// locals
+import { createGunzip } from 'zlib';
 import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 export async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
@@ -27,8 +26,6 @@ export async function* indexGff3({ config, attributesToIndex, inLocation, outDir
         const [seq_id, , type, start, end, , , , col9] = line.split('\t');
         const locStr = `${seq_id}:${start}..${end}`;
         if (!featureTypesToExclude.includes(type)) {
-            // turns gff3 attrs into a map, and converts the arrays into space
-            // separated strings
             const col9attrs = Object.fromEntries(col9
                 .split(';')
                 .map(f => f.trim())

package/esm/types/vcfAdapter.js

@@ -1,6 +1,5 @@
-import { createGunzip } from 'zlib';
 import readline from 'readline';
-// locals
+import { createGunzip } from 'zlib';
 import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
 export async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
@@ -21,10 +20,7 @@ export async function* indexVcf({ config, attributesToIndex, inLocation, outDir,
         if (line.startsWith('#')) {
             continue;
         }
-        // eslint-disable-next-line @typescript-eslint/no-unused-vars
         const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        // turns gff3 attrs into a map, and converts the arrays into space
-        // separated strings
         const fields = Object.fromEntries(info
             .split(';')
             .map(f => f.trim())

package/esm/util.js

@@ -1,6 +1,6 @@
+import path from 'path';
 import { isSupportedIndexingAdapter } from '@jbrowse/core/util';
 import sanitize from 'sanitize-filename';
-import path from 'path';
 export function createTextSearchConf(name, trackIds, assemblyNames, locationPath) {
     const base = path.join(locationPath, 'trix');
     const n = sanitize(name);
@@ -40,7 +40,6 @@ export function decodeURIComponentNoThrow(uri) {
         return decodeURIComponent(uri);
     }
     catch (e) {
-        // avoid throwing exception on a failure to decode URI component
         return uri;
     }
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -42,7 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
-    "@jbrowse/core": "^2.17.0",
+    "@jbrowse/core": "^3.0.0",
     "ixixx": "^2.0.1",
     "node-fetch": "^2.6.0",
     "sanitize-filename": "^1.6.3"
@@ -58,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }