@jbrowse/plugin-legacy-jbrowse 4.3.0 → 5.0.0-beta.1

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -1,37 +1,25 @@
-import { objectHash } from '@jbrowse/core/util';
-import setValue from 'set-value';
-import getValue from "./get-value.js";
-import { isSource, isTrack } from "./util.js";
-export function parseJB1Json(config, url) {
-    if (typeof config === 'string') {
-        let parsedConf;
+/* eslint no-cond-assign: ["error", "except-parens"] */
+import getValue from './get-value.js';
+import setValue from './set-value.js';
+/**
+ * Parse a JBrowse 1 config file. A `trackList.json` is JSON; a `tracks.conf`
+ * is JBrowse 1's own INI-like format, whose `[section.subsection]` headers and
+ * `key.subkey = value` lines both address a dotted path.
+ */
+export function parseJb1(text, url = '') {
+    if (text.trimStart().startsWith('{')) {
         try {
-            parsedConf = JSON.parse(config);
+            return JSON.parse(text);
         }
         catch (error) {
-            throw new Error(`${error} when parsing configuration.`);
+            throw new Error(`${error} when parsing ${url || 'configuration'}`, {
+                cause: error,
+            });
         }
-        return regularizeConf(parsedConf, url);
     }
-    return regularizeConf(config, url);
+    return parseConf(text, url);
 }
-export function parseJB1Conf(config, url) {
-    let parsedConf;
-    try {
-        parsedConf = parse(config, url);
-    }
-    catch (error) {
-        throw new Error(`${error} when parsing configuration.`);
-    }
-    return regularizeConf(parsedConf, url);
-}
-function isAlwaysArray(varName) {
-    if (varName === 'include') {
-        return true;
-    }
-    return false;
-}
-function parse(text, url) {
+function parseConf(text, url) {
     let section = [];
     let keyPath;
     let operation;
@@ -57,15 +45,12 @@ function parse(text, url) {
                 }
                 const path = [...section, ...keyPath].join('.');
                 if (operation === '+=') {
-                    let existing = getValue(data, path);
-                    if (existing) {
-                        if (!Array.isArray(existing)) {
-                            existing = [existing];
-                        }
-                    }
-                    else {
-                        existing = [];
-                    }
+                    const prev = getValue(data, path);
+                    const existing = Array.isArray(prev)
+                        ? prev
+                        : prev
+                            ? [prev]
+                            : [];
                     existing.push(parsedValue);
                     parsedValue = existing;
                 }
@@ -78,7 +63,7 @@ function parse(text, url) {
                 setValue(data, path, parsedValue);
             }
             catch (e) {
-                throw new Error(`syntax error${url ? ` in ${url}` : ''}${lineNumber ? ` at line ${lineNumber - 1}` : ''}`);
+                throw new Error(`syntax error${url ? ` in ${url}` : ''}${lineNumber ? ` at line ${lineNumber - 1}` : ''}`, { cause: e });
             }
         }
     }
@@ -98,8 +83,8 @@ function parse(text, url) {
         else if ((match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))) {
             recordVal();
             keyPath = match[1].trim().split(/\s*\.\s*/);
-            [, , operation] = match;
-            if (isAlwaysArray([...section, ...keyPath].join('.'))) {
+            operation = match[2];
+            if ([...section, ...keyPath].join('.') === 'include') {
                 operation = '+=';
             }
             value = match[3].trim();
@@ -123,213 +108,3 @@ function parse(text, url) {
     recordVal();
     return data;
 }
-export function regularizeConf(conf, url) {
-    if (conf.tracks && !Array.isArray(conf.tracks)) {
-        if (isTrack(conf.tracks)) {
-            conf.tracks = [conf.tracks];
-        }
-        else {
-            const tracks = [];
-            for (const label of Object.keys(conf.tracks)) {
-                const track = conf.tracks[label];
-                if (isTrack(track)) {
-                    tracks.push(track);
-                }
-                else {
-                    tracks.push({ label, ...track });
-                }
-            }
-            conf.tracks = tracks;
-        }
-    }
-    const meta = conf.trackMetadata;
-    if (meta?.sources) {
-        if (typeof meta.sources === 'string') {
-            meta.sources = [meta.sources];
-        }
-        if (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) {
-            for (const track of conf.tracks) {
-                addBase.push(track);
-            }
-        }
-        if (conf.stores) {
-            for (const store of Object.values(conf.stores)) {
-                addBase.push(store);
-            }
-        }
-        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) {
-    if (!trackConfig) {
-        return '';
-    }
-    if (trackConfig.type?.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$/i.test(urlTemplate)) {
-        return 'JBrowse/Store/SeqFeature/TwoBit';
-    }
-    if (trackConfig.type?.endsWith('/Sequence')) {
-        return 'JBrowse/Store/Sequence/StaticChunked';
-    }
-    return '';
-}
-function synthesizeTrackStoreConfig(mainConf, trackConfig) {
-    const { urlTemplate = '' } = trackConfig;
-    const storeClass = trackConfig.storeClass
-        ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
-        : guessStoreClass(trackConfig, urlTemplate);
-    if (!storeClass) {
-        console.warn(`Unable to determine an appropriate data store to use with track '${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) &&
-            !mainConf.stores?.refseqs
-            ? 'refseqs'
-            : `store${objectHash(storeConf)}`;
-    if (!mainConf.stores) {
-        mainConf.stores = {};
-    }
-    mainConf.stores[storeConf.name] = storeConf;
-    trackConfig.store = storeConf.name;
-}

package/esm/JBrowse1Connection/jb1ToJb2.d.ts

@@ -1,4 +1,4 @@
-import type { RefSeqs, Track } from './types.ts';
+import type { Track } from './types.ts';
 interface Jb2Track {
     trackId: string;
     name: string;
@@ -6,9 +6,14 @@ interface Jb2Track {
     category?: string[];
     adapter?: Jb2Adapter;
     type?: string;
-    defaultRendering?: string;
+    displays?: {
+        type: string;
+        displayId: string;
+        defaultRendering: string;
+    }[];
 }
 interface Jb2Adapter {
+    [key: string]: unknown;
     type: string;
     features?: Jb2Feature[];
     bamLocation?: Jb2Location;
@@ -24,6 +29,7 @@ interface Jb2Adapter {
     gffLocation?: Jb2Location;
     gffGzLocation?: Jb2Location;
     gtfLocation?: Jb2Location;
+    bedLocation?: Jb2Location;
     bedGzLocation?: Jb2Location;
     index?: {
         location: Jb2Location;
@@ -44,5 +50,4 @@ interface Jb2Location {
     locationType?: string;
 }
 export declare function convertTrackConfig(jb1TrackConfig: Track, dataRoot: string): Jb2Track;
-export declare function createRefSeqsAdapter(refSeqs: string | RefSeqs): Promise<Jb2Adapter>;
 export {};