@jbrowse/plugin-legacy-jbrowse 4.2.1 → 5.0.0-beta.1

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -1,27 +1,51 @@
+/**
+ * #config JBrowse1Connection
+ *
+ * #example
+ * An entry in the config's `connections`, pointing at a JBrowse 1 data
+ * directory — the one holding `trackList.json` and `seq/`. Its tracks are
+ * translated to JBrowse 2 equivalents on connect, which is the path for serving
+ * an existing JBrowse 1 instance's data without re-processing it.
+ * ```js
+ * {
+ *   type: 'JBrowse1Connection',
+ *   connectionId: 'jbrowse1_example',
+ *   name: 'Legacy JBrowse 1 data',
+ *   assemblyNames: ['hg19'],
+ *   dataDirLocation: { uri: 'https://example.com/jbrowse1/data/' },
+ * }
+ * ```
+ */
 declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    dataDirLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
+    /**
+     * #slot
+     */
+    readonly dataDirLocation: {
+        readonly type: "fileLocation";
+        readonly defaultValue: {
+            readonly uri: "https://mysite.com/jbrowse/data/";
+            readonly locationType: "UriLocation";
         };
-        description: string;
+        readonly description: "the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/";
     };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: never[];
+    /**
+     * #slot
+     */
+    readonly assemblyNames: {
+        readonly description: "name of the assembly the connection belongs to, should be a single entry";
+        readonly type: "stringArray";
+        readonly defaultValue: readonly [];
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        type: string;
-        defaultValue: string;
-        description: string;
+    readonly name: {
+        readonly type: "string";
+        readonly defaultValue: "nameOfConnection";
+        readonly description: "a unique name for this connection";
     };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
+    readonly assemblyNames: {
+        readonly type: "stringArray";
+        readonly defaultValue: readonly [];
+        readonly description: "optional list of names of assemblies in this connection";
     };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
 export default JBrowse1Connection;

package/esm/JBrowse1Connection/configSchema.js

@@ -1,21 +1,47 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
-function x() { }
+/**
+ * #config JBrowse1Connection
+ *
+ * #example
+ * An entry in the config's `connections`, pointing at a JBrowse 1 data
+ * directory — the one holding `trackList.json` and `seq/`. Its tracks are
+ * translated to JBrowse 2 equivalents on connect, which is the path for serving
+ * an existing JBrowse 1 instance's data without re-processing it.
+ * ```js
+ * {
+ *   type: 'JBrowse1Connection',
+ *   connectionId: 'jbrowse1_example',
+ *   name: 'Legacy JBrowse 1 data',
+ *   assemblyNames: ['hg19'],
+ *   dataDirLocation: { uri: 'https://example.com/jbrowse1/data/' },
+ * }
+ * ```
+ */
 const JBrowse1Connection = ConfigurationSchema('JBrowse1Connection', {
+    /**
+     * #slot
+     */
     dataDirLocation: {
         type: 'fileLocation',
         defaultValue: {
-            uri: 'http://mysite.com/jbrowse/data/',
+            uri: 'https://mysite.com/jbrowse/data/',
             locationType: 'UriLocation',
         },
-        description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
+        description: 'the location of the JBrowse 1 data directory, often something like https://mysite.com/jbrowse/data/',
     },
+    /**
+     * #slot
+     */
     assemblyNames: {
         description: 'name of the assembly the connection belongs to, should be a single entry',
         type: 'stringArray',
         defaultValue: [],
     },
 }, {
+    /**
+     * #baseConfiguration
+     */
     baseConfiguration: baseConnectionConfig,
 });
 export default JBrowse1Connection;

package/esm/JBrowse1Connection/get-value.d.ts

@@ -1,10 +1 @@
-export interface Options {
-    default?: unknown;
-    separator?: string;
-    joinChar?: string;
-    join?: (segs: string[]) => string;
-    split?: (path: string) => string[];
-    isValid?: (key: string, target: {}) => boolean;
-}
-declare const getValue: (target: unknown, path: string | number | string[], options?: Options) => unknown;
-export default getValue;
+export default function getValue(target: Record<string, unknown>, path: string): unknown;

package/esm/JBrowse1Connection/get-value.js

@@ -1,84 +1,11 @@
-const isObject = v => v !== null && typeof v === 'object';
-const join = (segs, joinChar, options) => {
-    if (typeof options.join === 'function') {
-        return options.join(segs);
-    }
-    return segs[0] + joinChar + segs[1];
-};
-const split = (path, splitChar, options) => {
-    if (typeof options.split === 'function') {
-        return options.split(path);
-    }
-    return path.split(splitChar);
-};
-const isValid = (key, target = {}, options) => {
-    if (typeof options?.isValid === 'function') {
-        return options.isValid(key, target);
-    }
-    return true;
-};
-const isValidObject = (v) => {
-    return isObject(v) || typeof v === 'function';
-};
-const getValue = (target, path, options = {}) => {
-    if (!isObject(options)) {
-        options = { default: options };
-    }
-    if (!isValidObject(target)) {
-        return options.default !== undefined ? options.default : target;
-    }
-    if (typeof path === 'number') {
-        path = String(path);
-    }
-    const pathIsArray = Array.isArray(path);
-    const pathIsString = typeof path === 'string';
-    const splitChar = options.separator || '.';
-    const joinChar = options.joinChar || (typeof splitChar === 'string' ? splitChar : '.');
-    if (!pathIsString && !pathIsArray) {
-        return target;
-    }
-    if (target[path] !== undefined) {
-        return isValid(path, target, options) ? target[path] : options.default;
-    }
-    const segs = pathIsArray ? path : split(path, splitChar, options);
-    const len = segs.length;
-    let idx = 0;
-    do {
-        let prop = segs[idx];
-        if (typeof prop !== 'string') {
-            prop = String(prop);
-        }
-        while (prop.endsWith('\\')) {
-            prop = join([prop.slice(0, -1), segs[++idx] || ''], joinChar, options);
-        }
-        if (target[prop] !== undefined) {
-            if (!isValid(prop, target, options)) {
-                return options.default;
-            }
-            target = target[prop];
-        }
-        else {
-            let hasProp = false;
-            let n = idx + 1;
-            while (n < len) {
-                prop = join([prop, segs[n++]], joinChar, options);
-                if ((hasProp = target[prop] !== undefined)) {
-                    if (!isValid(prop, target, options)) {
-                        return options.default;
-                    }
-                    target = target[prop];
-                    idx = n - 1;
-                    break;
-                }
-            }
-            if (!hasProp) {
-                return options.default;
-            }
+// minimal nested getter, mirroring ./set-value.ts
+export default function getValue(target, path) {
+    let value = target;
+    for (const seg of path.split('.')) {
+        if (typeof value !== 'object' || value === null) {
+            return undefined;
         }
-    } while (++idx < len && isValidObject(target));
-    if (idx === len) {
-        return target;
+        value = value[seg];
     }
-    return options.default;
-};
-export default getValue;
+    return value;
+}

package/esm/JBrowse1Connection/index.js

@@ -1,6 +1,6 @@
 import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
-import configSchema from "./configSchema.js";
-import modelFactory from "./model.js";
+import configSchema from './configSchema.js';
+import modelFactory from './model.js';
 export default function JBrowse1ConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType({
         name: 'JBrowse1Connection',

package/esm/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -1,36 +1,9 @@
-import type { Config, JBLocation } from './types.ts';
-export declare function fetchJb1(dataRoot?: JBLocation, baseConfig?: Config, baseConfigRoot?: JBLocation): Promise<Config>;
-export declare function createFinalConfig(baseConfig: Config, defaults?: {
-    tracks: never[];
-    containerID: string;
-    dataRoot: string;
-    show_tracklist: boolean;
-    show_nav: boolean;
-    show_menu: boolean;
-    show_overview: boolean;
-    show_fullviewlink: boolean;
-    update_browser_title: boolean;
-    updateBrowserURL: boolean;
-    refSeqs: string;
-    include: string[];
-    nameUrl: string;
-    datasets: {
-        _DEFAULT_EXAMPLES: boolean;
-        volvox: {
-            url: string;
-            name: string;
-        };
-        modencode: {
-            url: string;
-            name: string;
-        };
-        yeast: {
-            url: string;
-            name: string;
-        };
-    };
-    highlightSearchedRegions: boolean;
-    highResolutionMode: string;
-}): Promise<Config>;
-export declare function fetchConfigFile(location: JBLocation): Promise<Config>;
-export declare function parseJb1(config: string, url?: string): Config;
+import type { Config } from './types.ts';
+import type { FileLocation } from '@jbrowse/core/util/types';
+/**
+ * Read the track list out of a JBrowse 1 data directory. Only the tracks and
+ * the data root survive: the rest of a JBrowse 1 config — display defaults,
+ * `refSeqs`, `nameUrl`, the synthesized `stores` — describes the JBrowse 1
+ * browser, which is not the thing being configured here.
+ */
+export declare function fetchJb1(dataDir: FileLocation): Promise<Config>;

package/esm/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,247 +1,78 @@
 import { openLocation } from '@jbrowse/core/util/io';
-import { parseJB1Conf, parseJB1Json, regularizeConf } from "./jb1ConfigParse.js";
-import { deepUpdate, fillTemplate } from "./util.js";
-function isUriLocation(location) {
-    return location.uri !== undefined;
+import { parseJb1 } from './jb1ConfigParse.js';
+import { fillTemplate, isTrack } from './util.js';
+// JBrowse 1 kept a data directory's track list in either or both of these, so
+// a missing one is normal rather than an error
+const TRACK_LISTS = ['trackList.json', 'tracks.conf'];
+/**
+ * Read the track list out of a JBrowse 1 data directory. Only the tracks and
+ * the data root survive: the rest of a JBrowse 1 config — display defaults,
+ * `refSeqs`, `nameUrl`, the synthesized `stores` — describes the JBrowse 1
+ * browser, which is not the thing being configured here.
+ */
+export async function fetchJb1(dataDir) {
+    const dataRoot = locationPath(dataDir).replace(/\/$/, '');
+    const tracks = [];
+    const seen = new Set();
+    async function read(path) {
+        if (seen.has(path)) {
+            return;
+        }
+        seen.add(path);
+        const config = await readConfig(dataDir, path);
+        if (!config) {
+            return;
+        }
+        tracks.push(...regularizeTracks(config.tracks, { dataRoot }));
+        const dir = path.replace(/\/[^/]*$/, '');
+        for (const include of [config.include ?? []].flat()) {
+            await read(/^\w[\w+.-]*:/.test(include) ? include : `${dir}/${include}`);
+        }
+    }
+    for (const name of TRACK_LISTS) {
+        await read(`${dataRoot}/${name}`);
+    }
+    return { dataRoot, tracks };
 }
-function isLocalPathLocation(location) {
-    return location.localPath !== undefined;
+function locationPath(location) {
+    return 'uri' in location
+        ? location.uri
+        : 'localPath' in location
+            ? location.localPath
+            : '';
 }
-export async function fetchJb1(dataRoot = { uri: '', locationType: 'UriLocation' }, baseConfig = {
-    include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
-}, baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
-    const protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
-    const dataRootReg = JSON.parse(JSON.stringify(dataRoot));
-    let dataRootLocation = '';
-    if (isUriLocation(dataRoot)) {
-        dataRootLocation = dataRoot.uri;
-    }
-    if (isLocalPathLocation(dataRoot)) {
-        dataRootLocation = dataRoot.localPath;
-    }
-    if (dataRootLocation.endsWith('/')) {
-        dataRootReg[protocol] = dataRootLocation.slice(0, -1);
-    }
-    if ((isUriLocation(baseConfigRoot) && baseConfigRoot.uri) ||
-        (isLocalPathLocation(baseConfigRoot) && baseConfigRoot.localPath)) {
-        const baseProtocol = 'uri' in baseConfigRoot ? 'uri' : 'localPath';
-        let baseConfigLocation = '';
-        if (isUriLocation(baseConfigRoot)) {
-            baseConfigLocation = baseConfigRoot.uri;
-        }
-        if (isLocalPathLocation(baseConfigRoot)) {
-            baseConfigLocation = baseConfigRoot.localPath;
-        }
-        if (baseConfigLocation.endsWith('/')) {
-            baseConfigLocation = baseConfigLocation.slice(0, -1);
-        }
-        let newConfig = {};
-        for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {
-            let fetchedConfig = null;
-            try {
-                fetchedConfig = await fetchConfigFile({
-                    [baseProtocol]: `${baseConfigLocation}/${conf}`,
-                });
-            }
-            catch (error) {
-                console.error(`tried to access ${baseConfigLocation}/${conf}, but failed`);
-            }
-            newConfig = mergeConfigs(newConfig, fetchedConfig) || {};
-        }
-        if (dataRootReg[protocol]) {
-            newConfig.dataRoot = dataRootReg[protocol];
-        }
-        return createFinalConfig(newConfig);
-    }
-    const newConfig = regularizeConf(baseConfig, window.location.href);
-    if (dataRootReg[protocol]) {
-        newConfig.dataRoot = dataRootReg[protocol];
-    }
-    return createFinalConfig(newConfig);
-}
-export async function createFinalConfig(baseConfig, defaults = configDefaults) {
-    const configWithDefaults = deepUpdate(structuredClone(defaults), baseConfig);
-    let finalConfig = await loadIncludes(configWithDefaults);
-    finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig;
-    fillTemplates(finalConfig, finalConfig);
-    validateConfig(finalConfig);
-    return finalConfig;
-}
-export async function fetchConfigFile(location) {
-    const result = await openLocation(location).readFile('utf8');
-    if (isUriLocation(location)) {
-        return parseJb1(result, location.uri);
-    }
-    if (isLocalPathLocation(location)) {
-        return parseJb1(result, location.localPath);
-    }
-    return parseJb1(result);
-}
-export function parseJb1(config, url = '') {
-    if (config.trim().startsWith('{')) {
-        return parseJB1Json(config, url);
-    }
-    return parseJB1Conf(config, url);
+async function readConfig(dataDir, path) {
+    const location = 'localPath' in dataDir
+        ? { localPath: path, locationType: 'LocalPathLocation' }
+        : { uri: path, locationType: 'UriLocation' };
+    let text;
+    try {
+        text = await openLocation(location).readFile('utf8');
+    }
+    catch {
+        return undefined;
+    }
+    return parseJb1(text, path);
 }
-function mergeConfigs(a, b) {
-    if (b === null) {
-        return null;
-    }
-    if (a === null) {
-        a = {};
-    }
-    for (const prop of Object.keys(b)) {
-        if (prop === 'tracks' && prop in a) {
-            const aTracks = a[prop] || [];
-            const bTracks = b[prop] || [];
-            if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
-                a[prop] = mergeTrackConfigs(aTracks, bTracks);
-            }
-            else {
-                throw new Error(`Track config has not been properly regularized: ${aTracks} ${bTracks}`);
-            }
-        }
-        else if (!noRecursiveMerge(prop) &&
-            prop in a &&
-            typeof b[prop] === 'object' &&
-            typeof a[prop] === 'object') {
-            a[prop] = deepUpdate(a[prop], b[prop]);
-        }
-        else if (prop === 'dataRoot') {
-            if (a[prop] === undefined ||
-                (a[prop] === 'data' && b[prop] !== undefined)) {
-                a[prop] = b[prop];
-            }
-        }
-        else if (a[prop] === undefined || b[prop] !== undefined) {
-            a[prop] = b[prop];
-        }
-    }
-    return a;
-}
-function mergeTrackConfigs(a, b) {
-    if (!b.length) {
-        return a;
-    }
-    const aTracks = {};
-    for (const [i, t] of a.entries()) {
-        t.index = i;
-        aTracks[t.label] = t;
-    }
-    for (const bT of b) {
-        const aT = aTracks[bT.label];
-        if (aT) {
-            mergeConfigs(aT, bT);
-        }
-        else {
-            a.push(bT);
-        }
-    }
-    return a;
-}
-async function loadIncludes(inputConfig) {
-    inputConfig = structuredClone(inputConfig);
-    async function loadRecur(config, upstreamConf) {
-        const sourceUrl = config.sourceUrl || config.baseUrl;
-        if (!sourceUrl) {
-            throw new Error(`Could not determine source URL: ${JSON.stringify(config)}`);
-        }
-        const newUpstreamConf = mergeConfigs(structuredClone(upstreamConf), config);
-        if (!newUpstreamConf) {
-            throw new Error('Problem merging configs');
-        }
-        const includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
-        config.include = undefined;
-        const loads = includes.map(async (include) => {
-            include.cacheBuster = inputConfig.cacheBuster;
-            const includedData = await fetchConfigFile({
-                uri: new URL(include.url, sourceUrl).href,
-                locationType: 'UriLocation',
-            });
-            return loadRecur(includedData, newUpstreamConf);
-        });
-        const includedDataObjects = await Promise.all(loads);
-        for (const includedData of includedDataObjects) {
-            config = mergeConfigs(config, includedData) || config;
-        }
-        return config;
-    }
-    return loadRecur(inputConfig, {});
-}
-function regularizeIncludes(includes) {
-    if (!includes) {
-        return [];
-    }
-    if (!Array.isArray(includes)) {
-        includes = [includes];
-    }
-    return includes.map((include) => {
-        if (typeof include === 'string') {
-            include = { url: include };
-        }
-        if (!('format' in include)) {
-            include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json';
-        }
-        if (include.format === 'JB_json' && !('version' in include)) {
-            include.version = 1;
-        }
-        return include;
+/**
+ * JBrowse 1 accepted `tracks` as an array, as a single track, or as an object
+ * keyed by label; let a track hold its settings in a `config` subobject; and
+ * let any string value interpolate `{dataRoot}`.
+ */
+function regularizeTracks(tracks, fillWith) {
+    const list = Array.isArray(tracks)
+        ? tracks
+        : !tracks
+            ? []
+            : isTrack(tracks)
+                ? [tracks]
+                : Object.entries(tracks).map(([label, track]) => ({ label, ...track }));
+    return list.map(track => {
+        const { config, ...rest } = track;
+        const flat = { ...config, ...rest };
+        return Object.fromEntries(Object.entries(flat).map(([key, value]) => [
+            key,
+            typeof value === 'string' ? fillTemplate(value, fillWith) : value,
+        ]));
     });
 }
-function fillTemplates(subconfig, config) {
-    if (!subconfig) {
-        return subconfig;
-    }
-    if (Array.isArray(subconfig)) {
-        for (let i = 0; i < subconfig.length; i += 1) {
-            subconfig[i] = fillTemplates(subconfig[i], config);
-        }
-    }
-    else if (typeof subconfig === 'object') {
-        const sub = subconfig;
-        for (const name of Object.keys(sub)) {
-            sub[name] = fillTemplates(sub[name], config);
-        }
-    }
-    else if (typeof subconfig === 'string') {
-        return fillTemplate(subconfig, config);
-    }
-    return subconfig;
-}
-function noRecursiveMerge(propName) {
-    return propName === 'datasets';
-}
-const configDefaults = {
-    tracks: [],
-    containerID: 'GenomeBrowser',
-    dataRoot: 'data',
-    show_tracklist: true,
-    show_nav: true,
-    show_menu: true,
-    show_overview: true,
-    show_fullviewlink: true,
-    update_browser_title: true,
-    updateBrowserURL: true,
-    refSeqs: '{dataRoot}/seq/refSeqs.json',
-    include: ['jbrowse.conf', 'jbrowse_conf.json'],
-    nameUrl: '{dataRoot}/names/root.json',
-    datasets: {
-        _DEFAULT_EXAMPLES: true,
-        volvox: { url: '?data=sample_data/json/volvox', name: 'Volvox Example' },
-        modencode: {
-            url: '?data=sample_data/json/modencode',
-            name: 'MODEncode Example',
-        },
-        yeast: { url: '?data=sample_data/json/yeast', name: 'Yeast Example' },
-    },
-    highlightSearchedRegions: false,
-    highResolutionMode: 'auto',
-};
-function validateConfig(config) {
-    if (!config.tracks) {
-        config.tracks = [];
-    }
-    if (!config.baseUrl) {
-        throw new Error('Must provide a `baseUrl` in configuration');
-    }
-}

package/esm/JBrowse1Connection/jb1ConfigParse.d.ts

@@ -1,4 +1,7 @@
 import type { Config } from './types.ts';
-export declare function parseJB1Json(config: Config | string, url: string): Config;
-export declare function parseJB1Conf(config: string, url: string): Config;
-export declare function regularizeConf(conf: Config, url: string): Config;
+/**
+ * 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 declare function parseJb1(text: string, url?: string): Config;