@jbrowse/text-indexing 2.13.1 → 2.15.0

package/dist/TextIndexing.d.ts

@@ -1,11 +1,11 @@
 import { Track, indexType } from './util';
 export declare function indexTracks(args: {
     tracks: Track[];
-    outLocation?: string;
+    outDir?: string;
     signal?: AbortSignal;
-    attributes?: string[];
-    assemblies?: string[];
-    exclude?: string[];
+    attributesToIndex?: string[];
+    assemblyNames?: string[];
+    featureTypesToExclude?: string[];
     indexType?: indexType;
     statusCallback: (message: string) => void;
 }): Promise<never[]>;

package/dist/TextIndexing.js

@@ -13,17 +13,32 @@ const common_1 = require("./types/common");
 const ixixx_1 = require("ixixx");
 const util_1 = require("@jbrowse/core/util");
 async function indexTracks(args) {
-    const { tracks, outLocation, attributes, exclude, assemblies, indexType, statusCallback, signal, } = args;
+    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, signal, } = args;
     const idxType = indexType || 'perTrack';
     (0, util_1.checkAbortSignal)(signal);
     await (idxType === 'perTrack'
-        ? perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal)
-        : aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal));
+        ? perTrackIndex({
+            tracks,
+            statusCallback,
+            outDir,
+            attributesToIndex,
+            featureTypesToExclude,
+            signal,
+        })
+        : aggregateIndex({
+            tracks,
+            statusCallback,
+            outDir,
+            attributesToIndex,
+            assemblyNames,
+            featureTypesToExclude,
+            signal,
+        }));
     (0, util_1.checkAbortSignal)(signal);
     return [];
 }
-async function perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal) {
-    const outFlag = outLocation || '.';
+async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, }) {
+    const outFlag = paramOutDir || '.';
     const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
     const outDir = path_1.default.dirname(confFilePath);
@@ -32,22 +47,24 @@ async function perTrackIndex(tracks, statusCallback, outLocation, attributes, ex
         fs_1.default.mkdirSync(trixDir);
     }
     // default settings
-    const attrs = attributes || ['Name', 'ID'];
-    const excludeTypes = exclude || ['exon', 'CDS'];
-    const force = true;
     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 { textSearching, trackId, assemblyNames } = trackConfig;
+        const { trackId, assemblyNames } = trackConfig;
         const id = `${trackId}-index`;
-        if ((textSearching === null || textSearching === void 0 ? void 0 : textSearching.textSearchAdapter) && !force) {
-            console.warn(`Note: ${trackId} has already been indexed with this configuration, use --force to overwrite this track. Skipping for now`);
-            continue;
-        }
-        await indexDriver([trackConfig], outDir, attrs, id, true, excludeTypes, assemblyNames, statusCallback, signal);
+        await indexDriver({
+            tracks: [trackConfig],
+            outDir,
+            attributesToIndex,
+            name: id,
+            featureTypesToExclude,
+            assemblyNames,
+            statusCallback,
+            signal,
+        });
     }
 }
-async function aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal) {
-    const outFlag = outLocation || '.';
+async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, assemblyNames, }) {
+    const outFlag = paramOutDir || '.';
     const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path_1.default.join(outFlag, 'config.json') : outFlag;
     const outDir = path_1.default.dirname(confFilePath);
@@ -55,70 +72,92 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
     if (!fs_1.default.existsSync(trixDir)) {
         fs_1.default.mkdirSync(trixDir);
     }
-    if (!assemblies) {
+    if (!assemblyNames) {
         throw new Error('No assemblies passed. Assmeblies required for aggregate indexes');
     }
-    for (const asm of assemblies) {
-        // console.log('Indexing assembly ' + asm + '...')
-        const id = asm + '-index';
-        // default settings
-        const attrs = attributes || ['Name', 'ID'];
-        const excludeTypes = exclude || ['exon', 'CDS'];
-        // const force = true
-        const quiet = true;
-        // supported tracks for given assembly
+    for (const asm of assemblyNames) {
+        const id = `${asm}-index`;
         const supportedTracks = tracks
             .filter(track => { var _a; return (0, util_1.isSupportedIndexingAdapter)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
             .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
-        await indexDriver(supportedTracks, outDir, attrs, id, quiet, excludeTypes, [asm], statusCallback, signal);
+        await indexDriver({
+            tracks: supportedTracks,
+            outDir: outDir,
+            attributesToIndex,
+            name: id,
+            featureTypesToExclude,
+            assemblyNames: [asm],
+            statusCallback,
+            signal,
+        });
     }
 }
-async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude, assemblyNames, statusCallback, signal) {
-    const readable = stream_1.Readable.from(indexFiles(tracks, attributes, idxLocation, quiet, exclude, statusCallback, signal));
+async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, signal, }) {
+    const readable = stream_1.Readable.from(indexFiles({
+        tracks,
+        attributesToIndex,
+        outDir,
+        featureTypesToExclude,
+        statusCallback,
+        signal,
+    }));
     statusCallback('Indexing files.');
-    const ixIxxStream = await runIxIxx(readable, idxLocation, name);
+    await runIxIxx(readable, outDir, name);
     (0, util_1.checkAbortSignal)(signal);
     await (0, common_1.generateMeta)({
         configs: tracks,
-        attributes,
-        outDir: idxLocation,
+        attributesToIndex,
+        outDir,
         name,
-        exclude,
+        featureTypesToExclude,
         assemblyNames,
     });
     (0, util_1.checkAbortSignal)(signal);
-    return ixIxxStream;
 }
-async function* indexFiles(tracks, attributes, outLocation, quiet, typesToExclude, statusCallback, signal) {
+async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTypesToExclude: edx1, statusCallback, }) {
     for (const track of tracks) {
         const { adapter, textSearching } = track;
-        const { type } = adapter;
-        const { indexingFeatureTypesToExclude: types = typesToExclude, indexingAttributes: attrs = attributes, } = textSearching || {};
-        // currently only supporting GFF3Tabix and VCFTabix
-        switch (type) {
-            case 'Gff3TabixAdapter': {
-                yield* (0, gff3Adapter_1.indexGff3)(track, attrs, getLoc('gffGzLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'Gff3Adapter': {
-                yield* (0, gff3Adapter_1.indexGff3)(track, attrs, getLoc('gffLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'VcfTabixAdapter': {
-                yield* (0, vcfAdapter_1.indexVcf)(track, attrs, getLoc('vcfGzLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'VcfAdapter': {
-                yield* (0, vcfAdapter_1.indexVcf)(track, attrs, getLoc('vcfLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            // No default
+        const { type } = adapter || {};
+        const { indexingFeatureTypesToExclude: featureTypesToExclude = edx1, indexingAttributes: attributesToIndex = idx1, } = textSearching || {};
+        let myTotalBytes;
+        if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
+            yield* (0, gff3Adapter_1.indexGff3)({
+                config: track,
+                attributesToIndex,
+                inLocation: getLoc('gffGzLocation', track),
+                outDir,
+                featureTypesToExclude,
+                onStart: totalBytes => {
+                    myTotalBytes = totalBytes;
+                },
+                onUpdate: progressBytes => {
+                    statusCallback(`${progressBytes}/${myTotalBytes}`);
+                },
+            });
+        }
+        else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
+            yield* (0, vcfAdapter_1.indexVcf)({
+                config: track,
+                attributesToIndex,
+                inLocation: getLoc('vcfGzLocation', track),
+                outDir,
+                onStart: totalBytes => {
+                    myTotalBytes = totalBytes;
+                },
+                onUpdate: progressBytes => {
+                    statusCallback(`${progressBytes}/${myTotalBytes}`);
+                },
+            });
         }
     }
     return;
 }
 function getLoc(attr, config) {
-    const elt = config.adapter[attr];
+    var _a;
+    const elt = (_a = config.adapter) === null || _a === void 0 ? void 0 : _a[attr];
+    if (!elt) {
+        throw new Error('none');
+    }
     return elt.uri || elt.localPath;
 }
 function runIxIxx(readStream, idxLocation, name) {

package/dist/index.d.ts

@@ -1,2 +1,5 @@
 export * from './util';
+export * from './types/common';
 export { indexTracks } from './TextIndexing';
+export { indexGff3 } from './types/gff3Adapter';
+export { indexVcf } from './types/vcfAdapter';

package/dist/index.js

@@ -14,7 +14,12 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
     for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.indexTracks = void 0;
+exports.indexVcf = exports.indexGff3 = exports.indexTracks = void 0;
 __exportStar(require("./util"), exports);
+__exportStar(require("./types/common"), exports);
 var TextIndexing_1 = require("./TextIndexing");
 Object.defineProperty(exports, "indexTracks", { enumerable: true, get: function () { return TextIndexing_1.indexTracks; } });
+var gff3Adapter_1 = require("./types/gff3Adapter");
+Object.defineProperty(exports, "indexGff3", { enumerable: true, get: function () { return gff3Adapter_1.indexGff3; } });
+var vcfAdapter_1 = require("./types/vcfAdapter");
+Object.defineProperty(exports, "indexVcf", { enumerable: true, get: function () { return vcfAdapter_1.indexVcf; } });

package/dist/types/common.d.ts

@@ -5,23 +5,21 @@ export declare function createRemoteStream(urlIn: string): Promise<fetch.Respons
 export declare function isURL(FileName: string): boolean;
 export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
     totalBytes: number;
-    stream: NodeJS.ReadableStream | fs.ReadStream;
+    stream: NodeJS.ReadableStream;
+} | {
+    totalBytes: number;
+    stream: 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)
- * @param name -  assembly name or trackId
- * @param attributes -  attributes indexed
- * @param include -  feature types included from index
- * @param exclude -  feature types excluded from index
- * @param configs - list of track
  */
-export declare function generateMeta({ configs, attributes, outDir, name, exclude, assemblyNames, }: {
+export declare function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }: {
     configs: Track[];
-    attributes: string[];
+    attributesToIndex: string[];
     outDir: string;
     name: string;
-    exclude: string[];
+    featureTypesToExclude: string[];
     assemblyNames: string[];
 }): Promise<void>;

package/dist/types/common.js

@@ -12,15 +12,14 @@ 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.
+// 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.
 async function createRemoteStream(urlIn) {
-    const response = await (0, node_fetch_1.default)(urlIn);
-    if (!response.ok) {
-        throw new Error(`Failed to fetch ${urlIn} status ${response.status} ${response.statusText}`);
+    const res = await (0, node_fetch_1.default)(urlIn);
+    if (!res.ok) {
+        throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
     }
-    return response;
+    return res;
 }
 // Checks if the passed in string is a valid URL.
 // Returns a boolean.
@@ -35,20 +34,20 @@ function isURL(FileName) {
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
 async function getLocalOrRemoteStream(uri, out) {
-    var _a;
-    let stream;
-    let totalBytes = 0;
     if (isURL(uri)) {
         const result = await createRemoteStream(uri);
-        totalBytes = +(((_a = result.headers) === null || _a === void 0 ? void 0 : _a.get('Content-Length')) || 0);
-        stream = result.body;
+        return {
+            totalBytes: +(result.headers.get('Content-Length') || 0),
+            stream: result.body,
+        };
     }
     else {
         const filename = path_1.default.isAbsolute(uri) ? uri : path_1.default.join(out, uri);
-        totalBytes = fs_1.default.statSync(filename).size;
-        stream = fs_1.default.createReadStream(filename);
+        return {
+            totalBytes: fs_1.default.statSync(filename).size,
+            stream: fs_1.default.createReadStream(filename),
+        };
     }
-    return { totalBytes, stream };
 }
 function makeLocation(location, protocol) {
     if (protocol === 'uri') {
@@ -127,27 +126,20 @@ function guessAdapterFromFileName(filePath) {
 }
 /**
  * Generates metadata of index given a filename (trackId or assembly)
- * @param name -  assembly name or trackId
- * @param attributes -  attributes indexed
- * @param include -  feature types included from index
- * @param exclude -  feature types excluded from index
- * @param configs - list of track
  */
-async function generateMeta({ configs, attributes, outDir, name, exclude, assemblyNames, }) {
-    const tracks = configs.map(config => {
-        const { trackId, textSearching, adapter } = config;
-        const includeExclude = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) || exclude;
-        const metaAttrs = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributes;
-        return {
-            trackId: trackId,
-            attributesIndexed: metaAttrs,
-            excludedTypes: includeExclude,
-            adapterConf: adapter,
-        };
-    });
+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(),
-        tracks,
+        tracks: configs.map(config => {
+            const { trackId, textSearching, adapter } = config;
+            return {
+                trackId,
+                attributesIndexed: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributesToIndex,
+                excludedTypes: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) ||
+                    featureTypesToExclude,
+                adapterConf: adapter,
+            };
+        }),
         assemblyNames,
     }, null, 2));
 }

package/dist/types/gff3Adapter.d.ts

@@ -1,2 +1,11 @@
-import { Track } from '../util';
-export declare function indexGff3(config: Track, attributes: string[], inLocation: string, outLocation: string, typesToExclude: string[], quiet: boolean, statusCallback: (message: string) => void, signal?: AbortSignal): AsyncGenerator<string, void, unknown>;
+export declare function indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }: {
+    config: {
+        trackId: string;
+    };
+    attributesToIndex: string[];
+    inLocation: string;
+    outDir: string;
+    featureTypesToExclude: string[];
+    onStart: (totalBytes: number) => void;
+    onUpdate: (progressBytes: number) => void;
+}): AsyncGenerator<string, void, unknown>;

package/dist/types/gff3Adapter.js

@@ -6,24 +6,26 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexGff3 = indexGff3;
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
+// locals
 const util_1 = require("../util");
 const common_1 = require("./common");
-const util_2 = require("@jbrowse/core/util");
-async function* indexGff3(config, attributes, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
+async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
     const { trackId } = config;
     let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outLocation);
+    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outDir);
+    onStart(totalBytes);
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
-        // send an update?
-        const progress = Math.round((receivedBytes / totalBytes) * 100);
-        statusCallback(`${progress}`);
+        onUpdate(receivedBytes);
     });
     const rl = readline_1.default.createInterface({
-        input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+        input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
     });
     for await (const line of rl) {
-        if (line.startsWith('#')) {
+        if (!line.trim()) {
+            continue;
+        }
+        else if (line.startsWith('#')) {
             continue;
         }
         else if (line.startsWith('>')) {
@@ -31,7 +33,7 @@ async function* indexGff3(config, attributes, inLocation, outLocation, typesToEx
         }
         const [seq_id, , type, start, end, , , , col9] = line.split('\t');
         const locStr = `${seq_id}:${start}..${end}`;
-        if (!typesToExclude.includes(type)) {
+        if (!featureTypesToExclude.includes(type)) {
             // turns gff3 attrs into a map, and converts the arrays into space
             // separated strings
             const col9attrs = Object.fromEntries(col9
@@ -41,9 +43,11 @@ async function* indexGff3(config, attributes, inLocation, outLocation, typesToEx
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' '),
+                val
+                    ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
+                    : undefined,
             ]));
-            const attrs = attributes
+            const attrs = attributesToIndex
                 .map(attr => col9attrs[attr])
                 .filter((f) => !!f);
             if (attrs.length) {
@@ -52,11 +56,8 @@ async function* indexGff3(config, attributes, inLocation, outLocation, typesToEx
                     encodeURIComponent(trackId),
                     ...attrs.map(a => encodeURIComponent(a)),
                 ]).replaceAll(',', '|');
-                // Check abort signal
-                (0, util_2.checkAbortSignal)(signal);
                 yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
             }
         }
     }
-    // console.log('done')
 }

package/dist/types/vcfAdapter.d.ts

@@ -1,2 +1,8 @@
-import { Track } from '../util';
-export declare function indexVcf(config: Track, attributesToIndex: string[], inLocation: string, outLocation: string, typesToExclude: string[], quiet: boolean, statusCallback: (message: string) => void, signal?: AbortSignal): AsyncGenerator<string, void, unknown>;
+export declare function indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }: {
+    config: any;
+    attributesToIndex: string[];
+    inLocation: string;
+    outDir: string;
+    onStart: (totalBytes: number) => void;
+    onUpdate: (progressBytes: number) => void;
+}): AsyncGenerator<string, void, unknown>;

package/dist/types/vcfAdapter.js

@@ -6,19 +6,19 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.indexVcf = indexVcf;
 const zlib_1 = require("zlib");
 const readline_1 = __importDefault(require("readline"));
+// locals
 const util_1 = require("../util");
 const common_1 = require("./common");
-const util_2 = require("@jbrowse/core/util");
-async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
+async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
     const { trackId } = config;
     let receivedBytes = 0;
-    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outLocation);
+    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outDir);
+    onStart(totalBytes);
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
-        const progress = Math.round((receivedBytes / totalBytes) * 100);
-        statusCallback(`${progress}`);
+        onUpdate(receivedBytes);
     });
-    const gzStream = inLocation.match(/.b?gz$/)
+    const gzStream = /.b?gz$/.exec(inLocation)
         ? stream.pipe((0, zlib_1.createGunzip)())
         : stream;
     const rl = readline_1.default.createInterface({
@@ -30,7 +30,7 @@ async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typ
         }
         // eslint-disable-next-line @typescript-eslint/no-unused-vars
         const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        // turns vcf info attrs into a map, and converts the arrays into space
+        // turns gff3 attrs into a map, and converts the arrays into space
         // separated strings
         const fields = Object.fromEntries(info
             .split(';')
@@ -60,8 +60,6 @@ async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typ
                 encodeURIComponent(id || ''),
                 ...infoAttrs.map(a => encodeURIComponent(a || '')),
             ]).replaceAll(',', '|');
-            // Check abort signal
-            (0, util_2.checkAbortSignal)(signal);
             yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
         }
     }

package/dist/util.d.ts

@@ -50,27 +50,37 @@ export interface Sequence {
     trackId: string;
     adapter: IndexedFastaAdapter | BgzipFastaAdapter | TwoBitAdapter | ChromeSizesAdapter | CustomSequenceAdapter;
 }
+type Loc = UriLocation | LocalPathLocation;
 export interface Gff3TabixAdapter {
     type: 'Gff3TabixAdapter';
-    gffGzLocation: UriLocation | LocalPathLocation;
+    gffGzLocation: Loc;
 }
 export interface Gff3Adapter {
     type: 'Gff3Adapter';
-    gffLocation: UriLocation | LocalPathLocation;
+    gffLocation: Loc;
 }
 export interface GtfAdapter {
     type: 'GtfAdapter';
-    gtfLocation: UriLocation | LocalPathLocation;
+    gtfLocation: Loc;
 }
 export interface VcfTabixAdapter {
     type: 'VcfTabixAdapter';
-    vcfGzLocation: UriLocation | LocalPathLocation;
+    vcfGzLocation: Loc;
 }
 export interface VcfAdapter {
     type: 'VcfAdapter';
-    vcfLocation: UriLocation | LocalPathLocation;
+    vcfLocation: Loc;
+}
+export interface Track {
+    adapter?: {
+        type: string;
+        [key: string]: unknown;
+    };
+    textSearching?: TextSearching;
+    name: string;
+    assemblyNames: string[];
+    trackId: string;
 }
-export type Track = Record<string, any>;
 export interface TextSearching {
     indexingFeatureTypesToExclude?: string[];
     indexingAttributes?: string[];
@@ -87,10 +97,10 @@ export interface TrixTextSearchAdapter {
 export interface Config {
     assemblies?: Assembly[];
     assembly?: Assembly;
-    configuration?: {};
+    configuration?: Record<string, unknown>;
     aggregateTextSearchAdapters?: TrixTextSearchAdapter[];
     connections?: unknown[];
-    defaultSession?: {};
+    defaultSession?: Record<string, unknown>;
     tracks?: Track[];
 }
 export type indexType = 'aggregate' | 'perTrack';
@@ -114,3 +124,4 @@ export declare function createTextSearchConf(name: string, trackIds: string[], a
 };
 export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[], assemblyName?: string): Track[];
 export declare function decodeURIComponentNoThrow(uri: string): string;
+export {};

package/esm/TextIndexing.d.ts

@@ -1,11 +1,11 @@
 import { Track, indexType } from './util';
 export declare function indexTracks(args: {
     tracks: Track[];
-    outLocation?: string;
+    outDir?: string;
     signal?: AbortSignal;
-    attributes?: string[];
-    assemblies?: string[];
-    exclude?: string[];
+    attributesToIndex?: string[];
+    assemblyNames?: string[];
+    featureTypesToExclude?: string[];
     indexType?: indexType;
     statusCallback: (message: string) => void;
 }): Promise<never[]>;

package/esm/TextIndexing.js

@@ -7,17 +7,32 @@ import { generateMeta } from './types/common';
 import { ixIxxStream } from 'ixixx';
 import { checkAbortSignal, isSupportedIndexingAdapter, } from '@jbrowse/core/util';
 export async function indexTracks(args) {
-    const { tracks, outLocation, attributes, exclude, assemblies, indexType, statusCallback, signal, } = args;
+    const { tracks, outDir, attributesToIndex, featureTypesToExclude, assemblyNames, indexType, statusCallback, signal, } = args;
     const idxType = indexType || 'perTrack';
     checkAbortSignal(signal);
     await (idxType === 'perTrack'
-        ? perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal)
-        : aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal));
+        ? perTrackIndex({
+            tracks,
+            statusCallback,
+            outDir,
+            attributesToIndex,
+            featureTypesToExclude,
+            signal,
+        })
+        : aggregateIndex({
+            tracks,
+            statusCallback,
+            outDir,
+            attributesToIndex,
+            assemblyNames,
+            featureTypesToExclude,
+            signal,
+        }));
     checkAbortSignal(signal);
     return [];
 }
-async function perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal) {
-    const outFlag = outLocation || '.';
+async function perTrackIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, }) {
+    const outFlag = paramOutDir || '.';
     const isDir = fs.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path.join(outFlag, 'config.json') : outFlag;
     const outDir = path.dirname(confFilePath);
@@ -26,22 +41,24 @@ async function perTrackIndex(tracks, statusCallback, outLocation, attributes, ex
         fs.mkdirSync(trixDir);
     }
     // default settings
-    const attrs = attributes || ['Name', 'ID'];
-    const excludeTypes = exclude || ['exon', 'CDS'];
-    const force = true;
     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 { textSearching, trackId, assemblyNames } = trackConfig;
+        const { trackId, assemblyNames } = trackConfig;
         const id = `${trackId}-index`;
-        if ((textSearching === null || textSearching === void 0 ? void 0 : textSearching.textSearchAdapter) && !force) {
-            console.warn(`Note: ${trackId} has already been indexed with this configuration, use --force to overwrite this track. Skipping for now`);
-            continue;
-        }
-        await indexDriver([trackConfig], outDir, attrs, id, true, excludeTypes, assemblyNames, statusCallback, signal);
+        await indexDriver({
+            tracks: [trackConfig],
+            outDir,
+            attributesToIndex,
+            name: id,
+            featureTypesToExclude,
+            assemblyNames,
+            statusCallback,
+            signal,
+        });
     }
 }
-async function aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal) {
-    const outFlag = outLocation || '.';
+async function aggregateIndex({ tracks, statusCallback, outDir: paramOutDir, attributesToIndex = ['Name', 'ID'], featureTypesToExclude = ['exon', 'CDS'], signal, assemblyNames, }) {
+    const outFlag = paramOutDir || '.';
     const isDir = fs.lstatSync(outFlag).isDirectory();
     const confFilePath = isDir ? path.join(outFlag, 'config.json') : outFlag;
     const outDir = path.dirname(confFilePath);
@@ -49,70 +66,92 @@ async function aggregateIndex(tracks, statusCallback, outLocation, attributes, a
     if (!fs.existsSync(trixDir)) {
         fs.mkdirSync(trixDir);
     }
-    if (!assemblies) {
+    if (!assemblyNames) {
         throw new Error('No assemblies passed. Assmeblies required for aggregate indexes');
     }
-    for (const asm of assemblies) {
-        // console.log('Indexing assembly ' + asm + '...')
-        const id = asm + '-index';
-        // default settings
-        const attrs = attributes || ['Name', 'ID'];
-        const excludeTypes = exclude || ['exon', 'CDS'];
-        // const force = true
-        const quiet = true;
-        // supported tracks for given assembly
+    for (const asm of assemblyNames) {
+        const id = `${asm}-index`;
         const supportedTracks = tracks
             .filter(track => { var _a; return isSupportedIndexingAdapter((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
             .filter(track => (asm ? track.assemblyNames.includes(asm) : true));
-        await indexDriver(supportedTracks, outDir, attrs, id, quiet, excludeTypes, [asm], statusCallback, signal);
+        await indexDriver({
+            tracks: supportedTracks,
+            outDir: outDir,
+            attributesToIndex,
+            name: id,
+            featureTypesToExclude,
+            assemblyNames: [asm],
+            statusCallback,
+            signal,
+        });
     }
 }
-async function indexDriver(tracks, idxLocation, attributes, name, quiet, exclude, assemblyNames, statusCallback, signal) {
-    const readable = Readable.from(indexFiles(tracks, attributes, idxLocation, quiet, exclude, statusCallback, signal));
+async function indexDriver({ tracks, outDir, attributesToIndex, name, featureTypesToExclude, assemblyNames, statusCallback, signal, }) {
+    const readable = Readable.from(indexFiles({
+        tracks,
+        attributesToIndex,
+        outDir,
+        featureTypesToExclude,
+        statusCallback,
+        signal,
+    }));
     statusCallback('Indexing files.');
-    const ixIxxStream = await runIxIxx(readable, idxLocation, name);
+    await runIxIxx(readable, outDir, name);
     checkAbortSignal(signal);
     await generateMeta({
         configs: tracks,
-        attributes,
-        outDir: idxLocation,
+        attributesToIndex,
+        outDir,
         name,
-        exclude,
+        featureTypesToExclude,
         assemblyNames,
     });
     checkAbortSignal(signal);
-    return ixIxxStream;
 }
-async function* indexFiles(tracks, attributes, outLocation, quiet, typesToExclude, statusCallback, signal) {
+async function* indexFiles({ tracks, attributesToIndex: idx1, outDir, featureTypesToExclude: edx1, statusCallback, }) {
     for (const track of tracks) {
         const { adapter, textSearching } = track;
-        const { type } = adapter;
-        const { indexingFeatureTypesToExclude: types = typesToExclude, indexingAttributes: attrs = attributes, } = textSearching || {};
-        // currently only supporting GFF3Tabix and VCFTabix
-        switch (type) {
-            case 'Gff3TabixAdapter': {
-                yield* indexGff3(track, attrs, getLoc('gffGzLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'Gff3Adapter': {
-                yield* indexGff3(track, attrs, getLoc('gffLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'VcfTabixAdapter': {
-                yield* indexVcf(track, attrs, getLoc('vcfGzLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            case 'VcfAdapter': {
-                yield* indexVcf(track, attrs, getLoc('vcfLocation', track), outLocation, types, quiet, statusCallback, signal);
-                break;
-            }
-            // No default
+        const { type } = adapter || {};
+        const { indexingFeatureTypesToExclude: featureTypesToExclude = edx1, indexingAttributes: attributesToIndex = idx1, } = textSearching || {};
+        let myTotalBytes;
+        if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
+            yield* indexGff3({
+                config: track,
+                attributesToIndex,
+                inLocation: getLoc('gffGzLocation', track),
+                outDir,
+                featureTypesToExclude,
+                onStart: totalBytes => {
+                    myTotalBytes = totalBytes;
+                },
+                onUpdate: progressBytes => {
+                    statusCallback(`${progressBytes}/${myTotalBytes}`);
+                },
+            });
+        }
+        else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
+            yield* indexVcf({
+                config: track,
+                attributesToIndex,
+                inLocation: getLoc('vcfGzLocation', track),
+                outDir,
+                onStart: totalBytes => {
+                    myTotalBytes = totalBytes;
+                },
+                onUpdate: progressBytes => {
+                    statusCallback(`${progressBytes}/${myTotalBytes}`);
+                },
+            });
         }
     }
     return;
 }
 function getLoc(attr, config) {
-    const elt = config.adapter[attr];
+    var _a;
+    const elt = (_a = config.adapter) === null || _a === void 0 ? void 0 : _a[attr];
+    if (!elt) {
+        throw new Error('none');
+    }
     return elt.uri || elt.localPath;
 }
 function runIxIxx(readStream, idxLocation, name) {

package/esm/index.d.ts

@@ -1,2 +1,5 @@
 export * from './util';
+export * from './types/common';
 export { indexTracks } from './TextIndexing';
+export { indexGff3 } from './types/gff3Adapter';
+export { indexVcf } from './types/vcfAdapter';

package/esm/index.js

@@ -1,2 +1,5 @@
 export * from './util';
+export * from './types/common';
 export { indexTracks } from './TextIndexing';
+export { indexGff3 } from './types/gff3Adapter';
+export { indexVcf } from './types/vcfAdapter';

package/esm/types/common.d.ts

@@ -5,23 +5,21 @@ export declare function createRemoteStream(urlIn: string): Promise<fetch.Respons
 export declare function isURL(FileName: string): boolean;
 export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
     totalBytes: number;
-    stream: NodeJS.ReadableStream | fs.ReadStream;
+    stream: NodeJS.ReadableStream;
+} | {
+    totalBytes: number;
+    stream: 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)
- * @param name -  assembly name or trackId
- * @param attributes -  attributes indexed
- * @param include -  feature types included from index
- * @param exclude -  feature types excluded from index
- * @param configs - list of track
  */
-export declare function generateMeta({ configs, attributes, outDir, name, exclude, assemblyNames, }: {
+export declare function generateMeta({ configs, attributesToIndex, outDir, name, featureTypesToExclude, assemblyNames, }: {
     configs: Track[];
-    attributes: string[];
+    attributesToIndex: string[];
     outDir: string;
     name: string;
-    exclude: string[];
+    featureTypesToExclude: string[];
     assemblyNames: string[];
 }): Promise<void>;

package/esm/types/common.js

@@ -1,15 +1,14 @@
 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.
+// 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.
 export async function createRemoteStream(urlIn) {
-    const response = await fetch(urlIn);
-    if (!response.ok) {
-        throw new Error(`Failed to fetch ${urlIn} status ${response.status} ${response.statusText}`);
+    const res = await fetch(urlIn);
+    if (!res.ok) {
+        throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
     }
-    return response;
+    return res;
 }
 // Checks if the passed in string is a valid URL.
 // Returns a boolean.
@@ -24,20 +23,20 @@ export function isURL(FileName) {
     return url.protocol === 'http:' || url.protocol === 'https:';
 }
 export async function getLocalOrRemoteStream(uri, out) {
-    var _a;
-    let stream;
-    let totalBytes = 0;
     if (isURL(uri)) {
         const result = await createRemoteStream(uri);
-        totalBytes = +(((_a = result.headers) === null || _a === void 0 ? void 0 : _a.get('Content-Length')) || 0);
-        stream = result.body;
+        return {
+            totalBytes: +(result.headers.get('Content-Length') || 0),
+            stream: result.body,
+        };
     }
     else {
         const filename = path.isAbsolute(uri) ? uri : path.join(out, uri);
-        totalBytes = fs.statSync(filename).size;
-        stream = fs.createReadStream(filename);
+        return {
+            totalBytes: fs.statSync(filename).size,
+            stream: fs.createReadStream(filename),
+        };
     }
-    return { totalBytes, stream };
 }
 export function makeLocation(location, protocol) {
     if (protocol === 'uri') {
@@ -116,27 +115,20 @@ export function guessAdapterFromFileName(filePath) {
 }
 /**
  * Generates metadata of index given a filename (trackId or assembly)
- * @param name -  assembly name or trackId
- * @param attributes -  attributes indexed
- * @param include -  feature types included from index
- * @param exclude -  feature types excluded from index
- * @param configs - list of track
  */
-export async function generateMeta({ configs, attributes, outDir, name, exclude, assemblyNames, }) {
-    const tracks = configs.map(config => {
-        const { trackId, textSearching, adapter } = config;
-        const includeExclude = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) || exclude;
-        const metaAttrs = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributes;
-        return {
-            trackId: trackId,
-            attributesIndexed: metaAttrs,
-            excludedTypes: includeExclude,
-            adapterConf: adapter,
-        };
-    });
+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(),
-        tracks,
+        tracks: configs.map(config => {
+            const { trackId, textSearching, adapter } = config;
+            return {
+                trackId,
+                attributesIndexed: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributesToIndex,
+                excludedTypes: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) ||
+                    featureTypesToExclude,
+                adapterConf: adapter,
+            };
+        }),
         assemblyNames,
     }, null, 2));
 }

package/esm/types/gff3Adapter.d.ts

@@ -1,2 +1,11 @@
-import { Track } from '../util';
-export declare function indexGff3(config: Track, attributes: string[], inLocation: string, outLocation: string, typesToExclude: string[], quiet: boolean, statusCallback: (message: string) => void, signal?: AbortSignal): AsyncGenerator<string, void, unknown>;
+export declare function indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }: {
+    config: {
+        trackId: string;
+    };
+    attributesToIndex: string[];
+    inLocation: string;
+    outDir: string;
+    featureTypesToExclude: string[];
+    onStart: (totalBytes: number) => void;
+    onUpdate: (progressBytes: number) => void;
+}): AsyncGenerator<string, void, unknown>;

package/esm/types/gff3Adapter.js

@@ -1,23 +1,25 @@
 import { createGunzip } from 'zlib';
 import readline from 'readline';
+// locals
 import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
-import { checkAbortSignal } from '@jbrowse/core/util';
-export async function* indexGff3(config, attributes, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
+export async function* indexGff3({ config, attributesToIndex, inLocation, outDir, featureTypesToExclude, onStart, onUpdate, }) {
     const { trackId } = config;
     let receivedBytes = 0;
-    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outLocation);
+    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outDir);
+    onStart(totalBytes);
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
-        // send an update?
-        const progress = Math.round((receivedBytes / totalBytes) * 100);
-        statusCallback(`${progress}`);
+        onUpdate(receivedBytes);
     });
     const rl = readline.createInterface({
-        input: inLocation.match(/.b?gz$/) ? stream.pipe(createGunzip()) : stream,
+        input: /.b?gz$/.exec(inLocation) ? stream.pipe(createGunzip()) : stream,
     });
     for await (const line of rl) {
-        if (line.startsWith('#')) {
+        if (!line.trim()) {
+            continue;
+        }
+        else if (line.startsWith('#')) {
             continue;
         }
         else if (line.startsWith('>')) {
@@ -25,7 +27,7 @@ export async function* indexGff3(config, attributes, inLocation, outLocation, ty
         }
         const [seq_id, , type, start, end, , , , col9] = line.split('\t');
         const locStr = `${seq_id}:${start}..${end}`;
-        if (!typesToExclude.includes(type)) {
+        if (!featureTypesToExclude.includes(type)) {
             // turns gff3 attrs into a map, and converts the arrays into space
             // separated strings
             const col9attrs = Object.fromEntries(col9
@@ -35,9 +37,11 @@ export async function* indexGff3(config, attributes, inLocation, outLocation, ty
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                decodeURIComponentNoThrow(val).trim().split(',').join(' '),
+                val
+                    ? decodeURIComponentNoThrow(val).trim().split(',').join(' ')
+                    : undefined,
             ]));
-            const attrs = attributes
+            const attrs = attributesToIndex
                 .map(attr => col9attrs[attr])
                 .filter((f) => !!f);
             if (attrs.length) {
@@ -46,11 +50,8 @@ export async function* indexGff3(config, attributes, inLocation, outLocation, ty
                     encodeURIComponent(trackId),
                     ...attrs.map(a => encodeURIComponent(a)),
                 ]).replaceAll(',', '|');
-                // Check abort signal
-                checkAbortSignal(signal);
                 yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
             }
         }
     }
-    // console.log('done')
 }

package/esm/types/vcfAdapter.d.ts

@@ -1,2 +1,8 @@
-import { Track } from '../util';
-export declare function indexVcf(config: Track, attributesToIndex: string[], inLocation: string, outLocation: string, typesToExclude: string[], quiet: boolean, statusCallback: (message: string) => void, signal?: AbortSignal): AsyncGenerator<string, void, unknown>;
+export declare function indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }: {
+    config: any;
+    attributesToIndex: string[];
+    inLocation: string;
+    outDir: string;
+    onStart: (totalBytes: number) => void;
+    onUpdate: (progressBytes: number) => void;
+}): AsyncGenerator<string, void, unknown>;

package/esm/types/vcfAdapter.js

@@ -1,18 +1,18 @@
 import { createGunzip } from 'zlib';
 import readline from 'readline';
+// locals
 import { decodeURIComponentNoThrow } from '../util';
 import { getLocalOrRemoteStream } from './common';
-import { checkAbortSignal } from '@jbrowse/core/util';
-export async function* indexVcf(config, attributesToIndex, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
+export async function* indexVcf({ config, attributesToIndex, inLocation, outDir, onStart, onUpdate, }) {
     const { trackId } = config;
     let receivedBytes = 0;
-    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outLocation);
+    const { totalBytes, stream } = await getLocalOrRemoteStream(inLocation, outDir);
+    onStart(totalBytes);
     stream.on('data', chunk => {
         receivedBytes += chunk.length;
-        const progress = Math.round((receivedBytes / totalBytes) * 100);
-        statusCallback(`${progress}`);
+        onUpdate(receivedBytes);
     });
-    const gzStream = inLocation.match(/.b?gz$/)
+    const gzStream = /.b?gz$/.exec(inLocation)
         ? stream.pipe(createGunzip())
         : stream;
     const rl = readline.createInterface({
@@ -24,7 +24,7 @@ export async function* indexVcf(config, attributesToIndex, inLocation, outLocati
         }
         // eslint-disable-next-line @typescript-eslint/no-unused-vars
         const [ref, pos, id, _ref, _alt, _qual, _filter, info] = line.split('\t');
-        // turns vcf info attrs into a map, and converts the arrays into space
+        // turns gff3 attrs into a map, and converts the arrays into space
         // separated strings
         const fields = Object.fromEntries(info
             .split(';')
@@ -54,8 +54,6 @@ export async function* indexVcf(config, attributesToIndex, inLocation, outLocati
                 encodeURIComponent(id || ''),
                 ...infoAttrs.map(a => encodeURIComponent(a || '')),
             ]).replaceAll(',', '|');
-            // Check abort signal
-            checkAbortSignal(signal);
             yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
         }
     }

package/esm/util.d.ts

@@ -50,27 +50,37 @@ export interface Sequence {
     trackId: string;
     adapter: IndexedFastaAdapter | BgzipFastaAdapter | TwoBitAdapter | ChromeSizesAdapter | CustomSequenceAdapter;
 }
+type Loc = UriLocation | LocalPathLocation;
 export interface Gff3TabixAdapter {
     type: 'Gff3TabixAdapter';
-    gffGzLocation: UriLocation | LocalPathLocation;
+    gffGzLocation: Loc;
 }
 export interface Gff3Adapter {
     type: 'Gff3Adapter';
-    gffLocation: UriLocation | LocalPathLocation;
+    gffLocation: Loc;
 }
 export interface GtfAdapter {
     type: 'GtfAdapter';
-    gtfLocation: UriLocation | LocalPathLocation;
+    gtfLocation: Loc;
 }
 export interface VcfTabixAdapter {
     type: 'VcfTabixAdapter';
-    vcfGzLocation: UriLocation | LocalPathLocation;
+    vcfGzLocation: Loc;
 }
 export interface VcfAdapter {
     type: 'VcfAdapter';
-    vcfLocation: UriLocation | LocalPathLocation;
+    vcfLocation: Loc;
+}
+export interface Track {
+    adapter?: {
+        type: string;
+        [key: string]: unknown;
+    };
+    textSearching?: TextSearching;
+    name: string;
+    assemblyNames: string[];
+    trackId: string;
 }
-export type Track = Record<string, any>;
 export interface TextSearching {
     indexingFeatureTypesToExclude?: string[];
     indexingAttributes?: string[];
@@ -87,10 +97,10 @@ export interface TrixTextSearchAdapter {
 export interface Config {
     assemblies?: Assembly[];
     assembly?: Assembly;
-    configuration?: {};
+    configuration?: Record<string, unknown>;
     aggregateTextSearchAdapters?: TrixTextSearchAdapter[];
     connections?: unknown[];
-    defaultSession?: {};
+    defaultSession?: Record<string, unknown>;
     tracks?: Track[];
 }
 export type indexType = 'aggregate' | 'perTrack';
@@ -114,3 +124,4 @@ export declare function createTextSearchConf(name: string, trackIds: string[], a
 };
 export declare function findTrackConfigsToIndex(tracks: Track[], trackIds: string[], assemblyName?: string): Track[];
 export declare function decodeURIComponentNoThrow(uri: string): string;
+export {};

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/text-indexing",
-  "version": "2.13.1",
+  "version": "2.15.0",
   "description": "JBrowse 2 text indexing for desktop",
   "keywords": [
     "jbrowse",
@@ -32,7 +32,7 @@
     "build:esm": "tsc --build tsconfig.build.esm.json",
     "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
     "build": "npm run build:esm && npm run build:commonjs",
-    "test": "cd ../..; jest packages/text-indexing",
+    "test": "cd ../..; jest --passWithNoTests packages/text-indexing",
     "clean": "rimraf dist esm *.tsbuildinfo",
     "prebuild": "yarn clean",
     "prepack": "yarn build && yarn useDist",
@@ -42,6 +42,7 @@
   },
   "dependencies": {
     "@babel/runtime": "^7.16.3",
+    "@jbrowse/core": "^2.15.0",
     "ixixx": "^2.0.1",
     "node-fetch": "^2.6.0",
     "sanitize-filename": "^1.6.3"
@@ -57,5 +58,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "87eeb1fbf8311dbf88d5e75b5a265f03beffdda8"
 }