@jbrowse/text-indexing 2.6.1

package/LICENSE

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package/dist/TextIndexing.d.ts

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

package/dist/TextIndexing.js

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+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.indexTracks = void 0;
+const fs_1 = __importDefault(require("fs"));
+const path_1 = __importDefault(require("path"));
+const stream_1 = require("stream");
+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("./util");
+const util_2 = require("@jbrowse/core/util");
+async function indexTracks(args) {
+    const { tracks, outLocation, attributes, exclude, assemblies, indexType, statusCallback, signal, } = args;
+    const idxType = indexType || 'perTrack';
+    (0, util_2.checkAbortSignal)(signal);
+    await (idxType === 'perTrack'
+        ? perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal)
+        : aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal));
+    (0, util_2.checkAbortSignal)(signal);
+    return [];
+}
+exports.indexTracks = indexTracks;
+async function perTrackIndex(tracks, statusCallback, outLocation, attributes, exclude, signal) {
+    const outFlag = outLocation || '.';
+    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);
+    const trixDir = path_1.default.join(outDir, 'trix');
+    if (!fs_1.default.existsSync(trixDir)) {
+        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.supportedIndexingAdapters)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); });
+    for (const trackConfig of supportedTracks) {
+        const { textSearching, 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);
+    }
+}
+async function aggregateIndex(tracks, statusCallback, outLocation, attributes, assemblies, exclude, signal) {
+    const outFlag = outLocation || '.';
+    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);
+    const trixDir = path_1.default.join(outDir, 'trix');
+    if (!fs_1.default.existsSync(trixDir)) {
+        fs_1.default.mkdirSync(trixDir);
+    }
+    if (!assemblies) {
+        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
+        const supportedTracks = tracks
+            .filter(track => { var _a; return (0, util_1.supportedIndexingAdapters)((_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);
+    }
+}
+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));
+    statusCallback('Indexing files.');
+    try {
+        const ixIxxStream = await runIxIxx(readable, idxLocation, name);
+        (0, util_2.checkAbortSignal)(signal);
+        await (0, common_1.generateMeta)({
+            configs: tracks,
+            attributes,
+            outDir: idxLocation,
+            name,
+            exclude,
+            assemblyNames,
+        });
+        (0, util_2.checkAbortSignal)(signal);
+        return ixIxxStream;
+    }
+    catch (e) {
+        throw e;
+    }
+}
+async function* indexFiles(tracks, attributes, outLocation, quiet, typesToExclude, statusCallback, signal) {
+    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
+        }
+    }
+    return;
+}
+function getLoc(attr, config) {
+    const elt = config.adapter[attr];
+    return elt.uri || elt.localPath;
+}
+function runIxIxx(readStream, idxLocation, name) {
+    const ixFilename = path_1.default.join(idxLocation, 'trix', `${name}.ix`);
+    const ixxFilename = path_1.default.join(idxLocation, 'trix', `${name}.ixx`);
+    return (0, ixixx_1.ixIxxStream)(readStream, ixFilename, ixxFilename);
+}

package/dist/index.d.ts

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+export * from './util';
+export { indexTracks } from './TextIndexing';

package/dist/index.js

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+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+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;
+__exportStar(require("./util"), exports);
+var TextIndexing_1 = require("./TextIndexing");
+Object.defineProperty(exports, "indexTracks", { enumerable: true, get: function () { return TextIndexing_1.indexTracks; } });

package/dist/types/common.d.ts

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+/// <reference types="node" />
+/// <reference types="node" />
+import fs from 'fs';
+import { LocalPathLocation, UriLocation, Track } from '../util';
+export declare function createRemoteStream(urlIn: string): Promise<import("node-fetch").Response>;
+export declare function isURL(FileName: string): boolean;
+export declare function getLocalOrRemoteStream(uri: string, out: string): Promise<{
+    totalBytes: number;
+    stream: 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)
+ * @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, }: {
+    configs: Track[];
+    attributes: string[];
+    outDir: string;
+    name: string;
+    exclude: string[];
+    assemblyNames: string[];
+}): Promise<void>;

package/dist/types/common.js

@@ -0,0 +1,154 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.generateMeta = exports.guessAdapterFromFileName = exports.makeLocation = exports.getLocalOrRemoteStream = exports.isURL = exports.createRemoteStream = void 0;
+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.
+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}`);
+    }
+    return response;
+}
+exports.createRemoteStream = createRemoteStream;
+// Checks if the passed in string is a valid URL.
+// Returns a boolean.
+function isURL(FileName) {
+    let url;
+    try {
+        url = new URL(FileName);
+    }
+    catch (_) {
+        return false;
+    }
+    return url.protocol === 'http:' || url.protocol === 'https:';
+}
+exports.isURL = isURL;
+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;
+    }
+    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, stream };
+}
+exports.getLocalOrRemoteStream = getLocalOrRemoteStream;
+function makeLocation(location, protocol) {
+    if (protocol === 'uri') {
+        return { uri: location, locationType: 'UriLocation' };
+    }
+    if (protocol === 'localPath') {
+        return {
+            localPath: path_1.default.resolve(location),
+            locationType: 'LocalPathLocation',
+        };
+    }
+    throw new Error(`invalid protocol ${protocol}`);
+}
+exports.makeLocation = makeLocation;
+function guessAdapterFromFileName(filePath) {
+    // const uri = isURL(filePath) ? filePath : path.resolve(filePath)
+    const protocol = isURL(filePath) ? 'uri' : 'localPath';
+    const name = path_1.default.basename(filePath);
+    if (/\.vcf\.b?gz$/i.test(filePath)) {
+        return {
+            trackId: name,
+            name: name,
+            assemblyNames: [],
+            adapter: {
+                type: 'VcfTabixAdapter',
+                vcfGzLocation: makeLocation(filePath, protocol),
+            },
+        };
+    }
+    else if (/\.gff3?\.b?gz$/i.test(filePath)) {
+        return {
+            trackId: name,
+            name,
+            assemblyNames: [],
+            adapter: {
+                type: 'Gff3TabixAdapter',
+                gffGzLocation: makeLocation(filePath, protocol),
+            },
+        };
+    }
+    else if (/\.gtf?$/i.test(filePath)) {
+        return {
+            trackId: name,
+            name,
+            assemblyNames: [],
+            adapter: {
+                type: 'GtfAdapter',
+                gtfLocation: makeLocation(filePath, protocol),
+            },
+        };
+    }
+    else if (/\.vcf$/i.test(filePath)) {
+        return {
+            trackId: name,
+            name,
+            assemblyNames: [],
+            adapter: {
+                type: 'VcfAdapter',
+                vcfLocation: makeLocation(filePath, protocol),
+            },
+        };
+    }
+    else if (/\.gff3?$/i.test(filePath)) {
+        return {
+            trackId: name,
+            name,
+            assemblyNames: [],
+            adapter: {
+                type: 'Gff3Adapter',
+                gffLocation: makeLocation(filePath, protocol),
+            },
+        };
+    }
+    else {
+        throw new Error(`Unsupported file type ${filePath}`);
+    }
+}
+exports.guessAdapterFromFileName = guessAdapterFromFileName;
+/**
+ * Generates metadata of index given a filename (trackId or assembly)
+ * @param name -  assembly name or trackId
+ * @param attributes -  attributes indexed
+ * @param include -  feature types included from index
+ * @param exclude -  feature types excluded from index
+ * @param configs - list of track
+ */
+async function generateMeta({ configs, attributes, outDir, name, exclude, assemblyNames, }) {
+    const tracks = configs.map(config => {
+        const { trackId, textSearching, adapter } = config;
+        const includeExclude = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) || exclude;
+        const metaAttrs = (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributes;
+        return {
+            trackId: trackId,
+            attributesIndexed: metaAttrs,
+            excludedTypes: includeExclude,
+            adapterConf: adapter,
+        };
+    });
+    fs_1.default.writeFileSync(path_1.default.join(outDir, 'trix', `${name}_meta.json`), JSON.stringify({
+        dateCreated: new Date().toISOString(),
+        tracks,
+        assemblyNames,
+    }, null, 2));
+}
+exports.generateMeta = generateMeta;

package/dist/types/gff3Adapter.d.ts

@@ -0,0 +1,2 @@
+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>;

package/dist/types/gff3Adapter.js

@@ -0,0 +1,62 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.indexGff3 = void 0;
+const zlib_1 = require("zlib");
+const readline_1 = __importDefault(require("readline"));
+const common_1 = require("./common");
+const util_1 = require("@jbrowse/core/util");
+async function* indexGff3(config, attributes, inLocation, outLocation, typesToExclude, quiet, statusCallback, signal) {
+    const { trackId } = config;
+    let receivedBytes = 0;
+    const { totalBytes, stream } = await (0, common_1.getLocalOrRemoteStream)(inLocation, outLocation);
+    stream.on('data', chunk => {
+        receivedBytes += chunk.length;
+        // send an update?
+        const progress = Math.round((receivedBytes / totalBytes) * 100);
+        statusCallback(`${progress}`);
+    });
+    const rl = readline_1.default.createInterface({
+        input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+    });
+    for await (const line of rl) {
+        if (line.startsWith('#')) {
+            continue;
+        }
+        else if (line.startsWith('>')) {
+            break;
+        }
+        const [seq_id, , type, start, end, , , , col9] = line.split('\t');
+        const locStr = `${seq_id}:${start}..${end}`;
+        if (!typesToExclude.includes(type)) {
+            // turns gff3 attrs into a map, and converts the arrays into space
+            // separated strings
+            const col9attrs = Object.fromEntries(col9
+                .split(';')
+                .map(f => f.trim())
+                .filter(f => !!f)
+                .map(f => f.split('='))
+                .map(([key, val]) => [
+                key.trim(),
+                decodeURIComponent(val).trim().split(',').join(' '),
+            ]));
+            const attrs = attributes
+                .map(attr => col9attrs[attr])
+                .filter((f) => !!f);
+            if (attrs.length) {
+                const record = JSON.stringify([
+                    encodeURIComponent(locStr),
+                    encodeURIComponent(trackId),
+                    ...attrs.map(a => encodeURIComponent(a)),
+                ]).replaceAll(',', '|');
+                // Check abort signal
+                (0, util_1.checkAbortSignal)(signal);
+                yield `${record} ${[...new Set(attrs)].join(' ')}\n`;
+            }
+        }
+    }
+    // console.log('done')
+}
+exports.indexGff3 = indexGff3;

package/dist/types/vcfAdapter.d.ts

@@ -0,0 +1,2 @@
+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>;