@jbrowse/plugin-legacy-jbrowse 3.7.0 → 4.0.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -15,42 +15,35 @@
     "directory": "plugins/legacy-jbrowse"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/legacy-jbrowse",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@gmod/nclist": "^3.0.0",
-    "@jbrowse/core": "^3.7.0",
-    "crc": "^4.0.0",
-    "generic-filehandle2": "^2.0.1",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0",
-    "set-value": "^4.0.1"
+    "@gmod/nclist": "^3.0.4",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "generic-filehandle2": "^2.0.18",
+    "mobx": "^6.15.0",
+    "rxjs": "^7.8.2",
+    "set-value": "^4.1.0",
+    "@jbrowse/core": "^4.0.1"
   },
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/legacy-jbrowse",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}

package/dist/GuessNCList/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function GuessNCListF(pluginManager: PluginManager): void;

package/dist/GuessNCList/index.js

@@ -1,18 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.default = GuessNCListF;
-const tracks_1 = require("@jbrowse/core/util/tracks");
-function GuessNCListF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = (0, tracks_1.getFileName)(file);
-            return (/trackData.jsonz?$/i.test(fileName) && !adapterHint) ||
-                adapterHint === 'NCListAdapter'
-                ? {
-                    type: 'NCListAdapter',
-                    rootUrlTemplate: file,
-                }
-                : adapterGuesser(file, index, adapterHint);
-        };
-    });
-}

package/dist/JBrowse1Connection/configSchema.d.ts

@@ -1,27 +0,0 @@
-declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    dataDirLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-        description: string;
-    };
-    assemblyNames: {
-        description: string;
-        type: string;
-        defaultValue: never[];
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    name: {
-        type: string;
-        defaultValue: string;
-        description: string;
-    };
-    assemblyNames: {
-        type: string;
-        defaultValue: never[];
-        description: string;
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "connectionId">>, undefined>>;
-export default JBrowse1Connection;

package/dist/JBrowse1Connection/configSchema.js

@@ -1,23 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
-function x() { }
-const JBrowse1Connection = (0, configuration_1.ConfigurationSchema)('JBrowse1Connection', {
-    dataDirLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: 'http://mysite.com/jbrowse/data/',
-            locationType: 'UriLocation',
-        },
-        description: 'the location of the JBrowse 1 data directory, often something like http://mysite.com/jbrowse/data/',
-    },
-    assemblyNames: {
-        description: 'name of the assembly the connection belongs to, should be a single entry',
-        type: 'stringArray',
-        defaultValue: [],
-    },
-}, {
-    baseConfiguration: models_1.baseConnectionConfig,
-});
-exports.default = JBrowse1Connection;

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

@@ -1,10 +0,0 @@
-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;

package/dist/JBrowse1Connection/get-value.js

@@ -1,86 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-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 === null || options === void 0 ? void 0 : 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;
-            }
-        }
-    } while (++idx < len && isValidObject(target));
-    if (idx === len) {
-        return target;
-    }
-    return options.default;
-};
-exports.default = getValue;

package/dist/JBrowse1Connection/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function JBrowse1ConnectionF(pluginManager: PluginManager): void;

package/dist/JBrowse1Connection/index.js

@@ -1,19 +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.default = JBrowse1ConnectionF;
-const ConnectionType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/ConnectionType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-const model_1 = __importDefault(require("./model"));
-function JBrowse1ConnectionF(pluginManager) {
-    pluginManager.addConnectionType(() => new ConnectionType_1.default({
-        name: 'JBrowse1Connection',
-        configSchema: configSchema_1.default,
-        stateModel: (0, model_1.default)(pluginManager),
-        displayName: 'JBrowse 1 Data',
-        description: 'A JBrowse 1 data directory',
-        url: '//jbrowse.org/',
-    }));
-}

package/dist/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -1,36 +0,0 @@
-import type { Config, JBLocation } from './types';
-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;

package/dist/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,253 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fetchJb1 = fetchJb1;
-exports.createFinalConfig = createFinalConfig;
-exports.fetchConfigFile = fetchConfigFile;
-exports.parseJb1 = parseJb1;
-const io_1 = require("@jbrowse/core/util/io");
-const jb1ConfigParse_1 = require("./jb1ConfigParse");
-const util_1 = require("./util");
-function isUriLocation(location) {
-    return location.uri !== undefined;
-}
-function isLocalPathLocation(location) {
-    return location.localPath !== undefined;
-}
-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 = (0, jb1ConfigParse_1.regularizeConf)(baseConfig, window.location.href);
-    if (dataRootReg[protocol]) {
-        newConfig.dataRoot = dataRootReg[protocol];
-    }
-    return createFinalConfig(newConfig);
-}
-async function createFinalConfig(baseConfig, defaults = configDefaults) {
-    const configWithDefaults = (0, util_1.deepUpdate)(structuredClone(defaults), baseConfig);
-    let finalConfig = await loadIncludes(configWithDefaults);
-    finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig;
-    fillTemplates(finalConfig, finalConfig);
-    validateConfig(finalConfig);
-    return finalConfig;
-}
-async function fetchConfigFile(location) {
-    const result = await (0, io_1.openLocation)(location).readFile('utf8');
-    if (isUriLocation(location)) {
-        return parseJb1(result, location.uri);
-    }
-    if (isLocalPathLocation(location)) {
-        return parseJb1(result, location.localPath);
-    }
-    return parseJb1(result);
-}
-function parseJb1(config, url = '') {
-    if (config.trim().startsWith('{')) {
-        return (0, jb1ConfigParse_1.parseJB1Json)(config, url);
-    }
-    return (0, jb1ConfigParse_1.parseJB1Conf)(config, url);
-}
-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] = (0, util_1.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;
-    });
-}
-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 (0, util_1.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/dist/JBrowse1Connection/jb1ConfigParse.d.ts

@@ -1,4 +0,0 @@
-import type { Config } from './types';
-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;