@jbrowse/plugin-legacy-jbrowse 3.6.5 → 4.0.0

package/esm/NCListAdapter/NCListAdapter.js

@@ -3,8 +3,10 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { RemoteFile } from 'generic-filehandle2';
-import NCListFeature from './NCListFeature';
+import NCListFeature from "./NCListFeature.js";
 export default class NCListAdapter extends BaseFeatureDataAdapter {
+    nclist;
+    configRefNames;
     constructor(config, getSubAdapter, pluginManager) {
         super(config, getSubAdapter, pluginManager);
         const refNames = this.getConf('refNames');
@@ -13,9 +15,9 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         this.nclist = new NCListStore({
             baseUrl: '',
             urlTemplate: rootUrlTemplate.uri,
-            readFile: (url) => new RemoteFile(String(rootUrlTemplate.baseUri
+            readFile: (url) => new RemoteFile(rootUrlTemplate.baseUri
                 ? new URL(url, rootUrlTemplate.baseUri).toString()
-                : url)).readFile(),
+                : url).readFile(),
         });
     }
     getFeatures(region, opts = {}) {
@@ -32,9 +34,8 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
         return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
     }
     async hasDataForRefName(refName) {
-        var _a;
         const root = await this.nclist.getDataRoot(refName);
-        return !!((_a = root === null || root === void 0 ? void 0 : root.stats) === null || _a === void 0 ? void 0 : _a.featureCount);
+        return !!root?.stats?.featureCount;
     }
     async getRefNames() {
         return this.configRefNames || [];

package/esm/NCListAdapter/NCListFeature.js

@@ -1,6 +1,9 @@
 const jb2ToJb1 = { refName: 'seq_id' };
 const jb1ToJb2 = { seq_id: 'refName' };
 export default class NCListFeature {
+    ncFeature;
+    parentHandle;
+    uniqueId;
     constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();

package/esm/NCListAdapter/configSchema.d.ts

@@ -1,4 +1,4 @@
-declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+declare const NCListAdapter: import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaType<{
     rootUrlTemplate: {
         type: string;
         defaultValue: {
@@ -11,5 +11,5 @@ declare const NCListAdapter: import("@jbrowse/core/configuration/configurationSc
         defaultValue: never[];
         description: string;
     };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("node_modules/@jbrowse/core/src/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default NCListAdapter;

package/esm/NCListAdapter/index.js

@@ -1,5 +1,5 @@
 import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import configSchema from './configSchema';
+import configSchema from "./configSchema.js";
 export default function NCListAdapterF(pluginManager) {
     pluginManager.addAdapterType(() => new AdapterType({
         name: 'NCListAdapter',
@@ -8,6 +8,6 @@ export default function NCListAdapterF(pluginManager) {
         adapterMetadata: {
             category: 'Uncommon',
         },
-        getAdapterClass: () => import('./NCListAdapter').then(r => r.default),
+        getAdapterClass: () => import("./NCListAdapter.js").then(r => r.default),
     }));
 }

package/esm/index.js

@@ -1,13 +1,10 @@
 import Plugin from '@jbrowse/core/Plugin';
-import GuessNCListF from './GuessNCList';
-import JBrowse1ConnectionF from './JBrowse1Connection';
-import JBrowse1TextSearchAdapterF from './JBrowse1TextSearchAdapter';
-import NCListAdapterF from './NCListAdapter';
+import GuessNCListF from "./GuessNCList/index.js";
+import JBrowse1ConnectionF from "./JBrowse1Connection/index.js";
+import JBrowse1TextSearchAdapterF from "./JBrowse1TextSearchAdapter/index.js";
+import NCListAdapterF from "./NCListAdapter/index.js";
 export default class LegacyJBrowsePlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'LegacyJBrowsePlugin';
-    }
+    name = 'LegacyJBrowsePlugin';
     install(pluginManager) {
         NCListAdapterF(pluginManager);
         GuessNCListF(pluginManager);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "3.6.5",
+  "version": "4.0.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -15,43 +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": "^3.6.5",
-    "crc": "^4.0.0",
-    "generic-filehandle2": "^2.0.1",
-    "get-value": "^3.0.0",
-    "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": "^4.0.0"
   },
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "354d0a87b757b4d84f824b47507662f6f3a1693f"
-}
+  "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/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;