@jbrowse/plugin-legacy-jbrowse 3.6.5 → 4.0.0

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -1,341 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseJB1Json = parseJB1Json;
-exports.parseJB1Conf = parseJB1Conf;
-exports.regularizeConf = regularizeConf;
-const util_1 = require("@jbrowse/core/util");
-const get_value_1 = __importDefault(require("get-value"));
-const set_value_1 = __importDefault(require("set-value"));
-const util_2 = require("./util");
-function parseJB1Json(config, url) {
-    if (typeof config === 'string') {
-        let parsedConf;
-        try {
-            parsedConf = JSON.parse(config);
-        }
-        catch (error) {
-            throw new Error(`${error} when parsing configuration.`);
-        }
-        return regularizeConf(parsedConf, url);
-    }
-    return regularizeConf(config, url);
-}
-function parseJB1Conf(config, url) {
-    let parsedConf;
-    try {
-        parsedConf = parse(config, url);
-    }
-    catch (error) {
-        throw new Error(`${error} when parsing configuration.`);
-    }
-    return regularizeConf(parsedConf, url);
-}
-function isAlwaysArray(varName) {
-    if (varName === 'include') {
-        return true;
-    }
-    return false;
-}
-function parse(text, url) {
-    let section = [];
-    let keyPath;
-    let operation;
-    let value;
-    const data = { tracks: {} };
-    let lineNumber;
-    function recordVal() {
-        if (value !== undefined) {
-            let parsedValue;
-            try {
-                const match = /^json:(.+)/i.exec(value);
-                if (match) {
-                    parsedValue = JSON.parse(match[1]);
-                }
-                else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
-                    parsedValue = Number.parseFloat(value.replaceAll(',', ''));
-                }
-                else {
-                    parsedValue = value;
-                }
-                if (!keyPath) {
-                    throw new Error(`Error parsing in section ${section.join(' - ')}`);
-                }
-                const path = [...section, ...keyPath].join('.');
-                if (operation === '+=') {
-                    let existing = (0, get_value_1.default)(data, path);
-                    if (existing) {
-                        if (!Array.isArray(existing)) {
-                            existing = [existing];
-                        }
-                    }
-                    else {
-                        existing = [];
-                    }
-                    existing.push(parsedValue);
-                    parsedValue = existing;
-                }
-                if (parsedValue === 'true') {
-                    parsedValue = true;
-                }
-                if (parsedValue === 'false') {
-                    parsedValue = false;
-                }
-                (0, set_value_1.default)(data, path, parsedValue);
-            }
-            catch (e) {
-                throw new Error(`syntax error${url ? ` in ${url}` : ''}${lineNumber ? ` at line ${lineNumber - 1}` : ''}`);
-            }
-        }
-    }
-    for (const [i, textLine] of text.split(/\n|\r\n|\r/).entries()) {
-        lineNumber = i + 1;
-        const line = textLine.replace(/^\s*#.+/, '');
-        let match;
-        if ((match = /^\s*\[([^\]]+)/.exec(line))) {
-            recordVal();
-            keyPath = undefined;
-            value = undefined;
-            section = match[1].trim().split(/\s*\.\s*/);
-            if (section.length === 1 && section[0].toLowerCase() === 'general') {
-                section = [];
-            }
-        }
-        else if ((match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))) {
-            recordVal();
-            keyPath = match[1].trim().split(/\s*\.\s*/);
-            [, , operation] = match;
-            if (isAlwaysArray([...section, ...keyPath].join('.'))) {
-                operation = '+=';
-            }
-            value = match[3].trim();
-        }
-        else if (keyPath !== undefined &&
-            (match = /^\s{0,4}\+\s*(.+)/.exec(line))) {
-            recordVal();
-            operation = '+=';
-            value = match[1].trim();
-        }
-        else if (value !== undefined && (match = /^\s+(\S.*)/.exec(line))) {
-            const m = match[1];
-            value += value.length ? ` ${m.trim()}` : m.trim();
-        }
-        else {
-            recordVal();
-            keyPath = undefined;
-            value = undefined;
-        }
-    }
-    recordVal();
-    return data;
-}
-function regularizeConf(conf, url) {
-    if (conf.tracks && !Array.isArray(conf.tracks)) {
-        if ((0, util_2.isTrack)(conf.tracks)) {
-            conf.tracks = [conf.tracks];
-        }
-        else {
-            const tracks = [];
-            for (const label of Object.keys(conf.tracks)) {
-                const track = conf.tracks[label];
-                if ((0, util_2.isTrack)(track)) {
-                    tracks.push(track);
-                }
-                else {
-                    tracks.push({ label, ...track });
-                }
-            }
-            conf.tracks = tracks;
-        }
-    }
-    const meta = conf.trackMetadata;
-    if (meta === null || meta === void 0 ? void 0 : meta.sources) {
-        if (typeof meta.sources === 'string') {
-            meta.sources = [meta.sources];
-        }
-        if ((0, util_2.isSource)(meta.sources)) {
-            meta.sources = [meta.sources];
-        }
-        if (!Array.isArray(meta.sources)) {
-            const sources = [];
-            for (const name of Object.keys(meta.sources)) {
-                const source = meta.sources[name];
-                if (!('name' in source)) {
-                    source.name = name;
-                }
-                sources.push(source);
-            }
-            meta.sources = sources;
-        }
-        meta.sources = meta.sources.map((sourceDef) => {
-            if (typeof sourceDef === 'string') {
-                const newSourceDef = { url: sourceDef };
-                const typeMatch = /\.(\w+)$/.exec(sourceDef);
-                if (typeMatch) {
-                    newSourceDef.type = typeMatch[1].toLowerCase();
-                }
-                return newSourceDef;
-            }
-            return sourceDef;
-        });
-    }
-    conf.sourceUrl = conf.sourceUrl || url;
-    if (conf.sourceUrl.startsWith('/')) {
-        conf.sourceUrl = new URL(conf.sourceUrl, window.location.href).href;
-    }
-    conf.baseUrl = conf.baseUrl || new URL('.', conf.sourceUrl).href;
-    if (conf.baseUrl.length && !conf.baseUrl.endsWith('/')) {
-        conf.baseUrl += '/';
-    }
-    if (conf.sourceUrl) {
-        const addBase = [];
-        if (conf.tracks) {
-            addBase.push(...conf.tracks);
-        }
-        if (conf.stores) {
-            addBase.push(...Object.values(conf.stores));
-        }
-        if (conf.names) {
-            addBase.push(conf.names);
-        }
-        for (const t of addBase) {
-            if (!t.baseUrl) {
-                t.baseUrl = conf.baseUrl || '/';
-            }
-        }
-        if (conf.refSeqs && typeof conf.refSeqs === 'string') {
-            conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href;
-        }
-        if (conf.nameUrl) {
-            conf.nameUrl = new URL(conf.nameUrl, conf.sourceUrl).href;
-        }
-    }
-    conf.stores = conf.stores || {};
-    for (let trackConfig of conf.tracks || []) {
-        if (trackConfig.config) {
-            const c = trackConfig.config;
-            trackConfig.config = undefined;
-            trackConfig = { ...c, ...trackConfig };
-        }
-        if (trackConfig.store) {
-            continue;
-        }
-        let trackClassName;
-        if (trackConfig.type === 'FeatureTrack') {
-            trackClassName = 'JBrowse/View/Track/HTMLFeatures';
-        }
-        else if (trackConfig.type === 'ImageTrack') {
-            trackClassName = 'JBrowse/View/Track/FixedImage';
-        }
-        else if (trackConfig.type === 'ImageTrack.Wiggle') {
-            trackClassName = 'JBrowse/View/Track/FixedImage/Wiggle';
-        }
-        else if (trackConfig.type === 'SequenceTrack') {
-            trackClassName = 'JBrowse/View/Track/Sequence';
-        }
-        else {
-            trackClassName = regularizeClass('JBrowse/View/Track', trackConfig.type);
-        }
-        trackConfig.type = trackClassName;
-        synthesizeTrackStoreConfig(conf, trackConfig);
-        if (trackConfig.histograms) {
-            if (!trackConfig.histograms.baseUrl) {
-                trackConfig.histograms.baseUrl = trackConfig.baseUrl;
-            }
-            synthesizeTrackStoreConfig(conf, trackConfig.histograms);
-        }
-    }
-    return conf;
-}
-function regularizeClass(root, className) {
-    if (!className) {
-        return '';
-    }
-    if (!className.includes('/')) {
-        className = `${root}/${className}`;
-    }
-    className = className.replace(/^\//, '');
-    return className;
-}
-function guessStoreClass(trackConfig, urlTemplate) {
-    var _a, _b;
-    if (!trackConfig) {
-        return '';
-    }
-    if ((_a = trackConfig.type) === null || _a === void 0 ? void 0 : _a.includes('/FixedImage')) {
-        return `JBrowse/Store/TiledImage/Fixed${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
-    }
-    if (/\.jsonz?$/i.test(urlTemplate)) {
-        return `JBrowse/Store/SeqFeature/NCList${trackConfig.backendVersion === 0 ? '_v0' : ''}`;
-    }
-    if (/\.bam$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BAM';
-    }
-    if (/\.cram$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/CRAM';
-    }
-    if (/\.gff3?$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/GFF3';
-    }
-    if (/\.bed$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BED';
-    }
-    if (/\.vcf.b?gz$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/VCFTabix';
-    }
-    if (/\.gff3?.b?gz$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/GFF3Tabix';
-    }
-    if (/\.bed.b?gz$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BEDTabix';
-    }
-    if (/\.(bw|bigwig)$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BigWig';
-    }
-    if (/\.(bb|bigbed)$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BigBed';
-    }
-    if (/\.(fa|fasta)$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/IndexedFasta';
-    }
-    if (/\.(fa|fasta)\.b?gz$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/BgzipIndexedFasta';
-    }
-    if (/\.2bit$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/TwoBit';
-    }
-    if ((_b = trackConfig.type) === null || _b === void 0 ? void 0 : _b.endsWith('/Sequence')) {
-        return 'JBrowse/Store/Sequence/StaticChunked';
-    }
-    return '';
-}
-function synthesizeTrackStoreConfig(mainConf, trackConfig) {
-    var _a;
-    const { urlTemplate = '' } = trackConfig;
-    const storeClass = trackConfig.storeClass
-        ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
-        : guessStoreClass(trackConfig, urlTemplate);
-    if (!storeClass) {
-        console.warn(`Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`);
-        return;
-    }
-    const storeConf = { ...trackConfig, type: storeClass };
-    storeConf.name =
-        (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
-            storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
-            storeClass === 'JBrowse/Store/SeqFeature/IndexedFasta' ||
-            storeClass === 'JBrowse/Store/SeqFeature/BgzipIndexedFasta' ||
-            storeClass === 'JBrowse/Store/SeqFeature/TwoBit' ||
-            storeClass === 'JBrowse/Store/Sequence/TwoBit' ||
-            trackConfig.useAsRefSeqStore) &&
-            !((_a = mainConf.stores) === null || _a === void 0 ? void 0 : _a.refseqs)
-            ? 'refseqs'
-            : `store${(0, util_1.objectHash)(storeConf)}`;
-    if (!mainConf.stores) {
-        mainConf.stores = {};
-    }
-    mainConf.stores[storeConf.name] = storeConf;
-    trackConfig.store = storeConf.name;
-}

package/dist/JBrowse1Connection/jb1ToJb2.d.ts

@@ -1,49 +0,0 @@
-import type { RefSeqs, Track } from './types';
-interface Jb2Track {
-    trackId: string;
-    name: string;
-    description?: string;
-    category?: string[];
-    adapter?: Jb2Adapter;
-    type?: string;
-    defaultRendering?: string;
-}
-interface Jb2Adapter {
-    type: string;
-    features?: Jb2Feature[];
-    bamLocation?: Jb2Location;
-    cramLocation?: Jb2Location;
-    craiLocation?: Jb2Location;
-    fastaLocation?: Jb2Location;
-    faiLocation?: Jb2Location;
-    gziLocation?: Jb2Location;
-    twoBitLocation?: Jb2Location;
-    bigWigLocation?: Jb2Location;
-    bigBedLocation?: Jb2Location;
-    vcfGzLocation?: Jb2Location;
-    gffLocation?: Jb2Location;
-    gffGzLocation?: Jb2Location;
-    gtfLocation?: Jb2Location;
-    bedGzLocation?: Jb2Location;
-    index?: {
-        location: Jb2Location;
-        indexType?: string;
-    };
-    rootUrlTemplate?: Jb2Location;
-    sequenceAdapter?: Jb2Adapter;
-}
-interface Jb2Feature {
-    refName: string;
-    uniqueId: string;
-    start: number;
-    end: number;
-}
-interface Jb2Location {
-    uri?: string;
-    localPath?: string;
-    blobId?: string;
-    locationType?: string;
-}
-export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string, sequenceAdapter: Jb2Adapter): Jb2Track;
-export declare function createRefSeqsAdapter(refSeqs: string | RefSeqs): Promise<Jb2Adapter>;
-export {};