@jbrowse/plugin-legacy-jbrowse 2.17.0 → 3.0.0

package/dist/NCListAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -34,6 +44,9 @@ function NCListAdapterF(pluginManager) {
         name: 'NCListAdapter',
         displayName: 'NCList adapter',
         configSchema: configSchema_1.default,
+        adapterMetadata: {
+            category: 'Uncommon',
+        },
         getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./NCListAdapter'))).then(r => r.default),
     }));
 }

package/dist/index.d.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin';
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default class LegacyJBrowsePlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/dist/index.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
-const NCListAdapter_1 = __importDefault(require("./NCListAdapter"));
-const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
-const JBrowse1Connection_1 = __importDefault(require("./JBrowse1Connection"));
 const GuessNCList_1 = __importDefault(require("./GuessNCList"));
+const JBrowse1Connection_1 = __importDefault(require("./JBrowse1Connection"));
+const JBrowse1TextSearchAdapter_1 = __importDefault(require("./JBrowse1TextSearchAdapter"));
+const NCListAdapter_1 = __importDefault(require("./NCListAdapter"));
 class LegacyJBrowsePlugin extends Plugin_1.default {
     constructor() {
         super(...arguments);

package/esm/GuessNCList/index.d.ts

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

package/esm/GuessNCList/index.js

@@ -2,16 +2,14 @@ import { getFileName } from '@jbrowse/core/util/tracks';
 export default function GuessNCListF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /trackData.jsonz?$/i;
-            const adapterName = 'NCListAdapter';
             const fileName = getFileName(file);
-            if (regexGuess.test(fileName) || adapterHint === adapterName) {
-                return {
-                    type: adapterName,
+            return (/trackData.jsonz?$/i.test(fileName) && !adapterHint) ||
+                adapterHint === 'NCListAdapter'
+                ? {
+                    type: 'NCListAdapter',
                     rootUrlTemplate: file,
-                };
-            }
-            return adapterGuesser(file, index, adapterHint);
+                }
+                : adapterGuesser(file, index, adapterHint);
         };
     });
 }

package/esm/JBrowse1Connection/configSchema.d.ts

@@ -1,7 +1,4 @@
 declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     dataDirLocation: {
         type: string;
         defaultValue: {
@@ -10,9 +7,6 @@ declare const JBrowse1Connection: import("@jbrowse/core/configuration/configurat
         };
         description: string;
     };
-    /**
-     * #slot
-     */
     assemblyNames: {
         description: string;
         type: string;

package/esm/JBrowse1Connection/configSchema.js

@@ -1,13 +1,7 @@
-import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config JBrowse1Connection
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models';
+function x() { }
 const JBrowse1Connection = ConfigurationSchema('JBrowse1Connection', {
-    /**
-     * #slot
-     */
     dataDirLocation: {
         type: 'fileLocation',
         defaultValue: {
@@ -16,18 +10,12 @@ const JBrowse1Connection = ConfigurationSchema('JBrowse1Connection', {
         },
         description: 'the location of the JBrowse 1 data directory, often something like http://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/index.d.ts

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

package/esm/JBrowse1Connection/index.js

@@ -1,7 +1,6 @@
 import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType';
-// locals
-import modelFactory from './model';
 import configSchema from './configSchema';
+import modelFactory from './model';
 export default function JBrowse1ConnectionF(pluginManager) {
     pluginManager.addConnectionType(() => new ConnectionType({
         name: 'JBrowse1Connection',

package/esm/JBrowse1Connection/jb1ConfigLoad.d.ts

@@ -1,4 +1,4 @@
-import { JBLocation, Config } from './types';
+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[];

package/esm/JBrowse1Connection/jb1ConfigLoad.js

@@ -1,23 +1,15 @@
 import { openLocation } from '@jbrowse/core/util/io';
-import { parseJB1Json, parseJB1Conf, regularizeConf } from './jb1ConfigParse';
-import { clone, deepUpdate, fillTemplate } from './util';
+import { parseJB1Conf, parseJB1Json, regularizeConf } from './jb1ConfigParse';
+import { deepUpdate, fillTemplate } from './util';
 function isUriLocation(location) {
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     return location.uri !== undefined;
 }
 function isLocalPathLocation(location) {
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     return location.localPath !== undefined;
 }
-export async function fetchJb1(
-// eslint-disable-next-line unicorn/no-object-as-default-parameter
-dataRoot = { uri: '', locationType: 'UriLocation' }, 
-// eslint-disable-next-line unicorn/no-object-as-default-parameter
-baseConfig = {
+export async function fetchJb1(dataRoot = { uri: '', locationType: 'UriLocation' }, baseConfig = {
     include: ['{dataRoot}/trackList.json', '{dataRoot}/tracks.conf'],
-}, 
-// eslint-disable-next-line unicorn/no-object-as-default-parameter
-baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
+}, baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
     const protocol = 'uri' in dataRoot ? 'uri' : 'localPath';
     const dataRootReg = JSON.parse(JSON.stringify(dataRoot));
     let dataRootLocation = '';
@@ -47,7 +39,6 @@ baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
         for (const conf of ['jbrowse.conf', 'jbrowse_conf.json']) {
             let fetchedConfig = null;
             try {
-                // @ts-expect-error
                 fetchedConfig = await fetchConfigFile({
                     [baseProtocol]: `${baseConfigLocation}/${conf}`,
                 });
@@ -69,7 +60,7 @@ baseConfigRoot = { uri: '', locationType: 'UriLocation' }) {
     return createFinalConfig(newConfig);
 }
 export async function createFinalConfig(baseConfig, defaults = configDefaults) {
-    const configWithDefaults = deepUpdate(clone(defaults), baseConfig);
+    const configWithDefaults = deepUpdate(structuredClone(defaults), baseConfig);
     let finalConfig = await loadIncludes(configWithDefaults);
     finalConfig = mergeConfigs(finalConfig, baseConfig) || finalConfig;
     fillTemplates(finalConfig, finalConfig);
@@ -92,9 +83,6 @@ export function parseJb1(config, url = '') {
     }
     return parseJB1Conf(config, url);
 }
-/**
- * Merges config object b into a. Properties in b override those in a.
- */
 function mergeConfigs(a, b) {
     if (b === null) {
         return null;
@@ -115,11 +103,8 @@ function mergeConfigs(a, b) {
         }
         else if (!noRecursiveMerge(prop) &&
             prop in a &&
-            // @ts-expect-error
             typeof b[prop] === 'object' &&
-            // @ts-expect-error
             typeof a[prop] === 'object') {
-            // @ts-expect-error
             a[prop] = deepUpdate(a[prop], b[prop]);
         }
         else if (prop === 'dataRoot') {
@@ -127,23 +112,17 @@ function mergeConfigs(a, b) {
                 (a[prop] === 'data' && b[prop] !== undefined)) {
                 a[prop] = b[prop];
             }
-            // @ts-expect-error
         }
         else if (a[prop] === undefined || b[prop] !== undefined) {
-            // @ts-expect-error
             a[prop] = b[prop];
         }
     }
     return a;
 }
-/**
- * Special-case merging of two `tracks` configuration arrays.
- */
 function mergeTrackConfigs(a, b) {
     if (!b.length) {
         return a;
     }
-    // index the tracks in `a` by track label
     const aTracks = {};
     a.forEach((t, i) => {
         t.index = i;
@@ -160,19 +139,14 @@ function mergeTrackConfigs(a, b) {
     });
     return a;
 }
-/**
- * Recursively fetch, parse, and merge all the includes in the given config
- * object.  Calls the callback with the resulting configuration when finished.
- * @param inputConfig - Config to load includes into
- */
 async function loadIncludes(inputConfig) {
-    inputConfig = clone(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(clone(upstreamConf), config);
+        const newUpstreamConf = mergeConfigs(structuredClone(upstreamConf), config);
         if (!newUpstreamConf) {
             throw new Error('Problem merging configs');
         }
@@ -198,16 +172,13 @@ function regularizeIncludes(includes) {
     if (!includes) {
         return [];
     }
-    // coerce include to an array
     if (!Array.isArray(includes)) {
         includes = [includes];
     }
     return includes.map((include) => {
-        // coerce bare strings in the includes to URLs
         if (typeof include === 'string') {
             include = { url: include };
         }
-        // set defaults for format and version
         if (!('format' in include)) {
             include.format = include.url.endsWith('.conf') ? 'conf' : 'JB_json';
         }
@@ -233,15 +204,10 @@ function fillTemplates(subconfig, config) {
         }
     }
     else if (typeof subconfig === 'string') {
-        // @ts-expect-error
         return fillTemplate(subconfig, config);
     }
     return subconfig;
 }
-/**
- * list of config properties that should not be recursively merged
- * @param propName - name of config property
- */
 function noRecursiveMerge(propName) {
     return propName === 'datasets';
 }
@@ -271,11 +237,6 @@ const configDefaults = {
     highlightSearchedRegions: false,
     highResolutionMode: 'auto',
 };
-/**
- * Examine the loaded and merged configuration for errors.  Throws
- * exceptions if it finds anything amiss.
- * @returns nothing meaningful
- */
 function validateConfig(config) {
     if (!config.tracks) {
         config.tracks = [];

package/esm/JBrowse1Connection/jb1ConfigParse.d.ts

@@ -1,11 +1,4 @@
-import { Config } from './types';
+import type { Config } from './types';
 export declare function parseJB1Json(config: Config | string, url: string): Config;
 export declare function parseJB1Conf(config: string, url: string): Config;
-/**
- * Applies defaults and any other necessary tweaks to the loaded configuration.
- * @param conf - the object containing the configuration, which it modifies
- * in-place
- * @param url - URL of the config file
- * @returns the same object it was passed
- */
 export declare function regularizeConf(conf: Config, url: string): Config;

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -1,7 +1,6 @@
-/* eslint no-cond-assign: ["error", "except-parens"] */
+import { objectHash } from '@jbrowse/core/util';
 import getValue from 'get-value';
 import setValue from 'set-value';
-import { objectHash } from '@jbrowse/core/util';
 import { isSource, isTrack } from './util';
 export function parseJB1Json(config, url) {
     if (typeof config === 'string') {
@@ -43,12 +42,10 @@ function parse(text, url) {
         if (value !== undefined) {
             let parsedValue;
             try {
-                // parse json
                 const match = /^json:(.+)/i.exec(value);
                 if (match) {
                     parsedValue = JSON.parse(match[1]);
                 }
-                // parse numbers if it looks numeric
                 else if (/^[+-]?[\d.,]+([eE][-+]?\d+)?$/.test(value)) {
                     parsedValue = Number.parseFloat(value.replaceAll(',', ''));
                 }
@@ -88,10 +85,8 @@ function parse(text, url) {
     text.split(/\n|\r\n|\r/).forEach((textLine, i) => {
         lineNumber = i + 1;
         const line = textLine.replace(/^\s*#.+/, '');
-        // new section
         let match;
         if ((match = /^\s*\[([^\]]+)/.exec(line))) {
-            // new section
             recordVal();
             keyPath = undefined;
             value = undefined;
@@ -100,7 +95,6 @@ function parse(text, url) {
                 section = [];
             }
         }
-        // new value
         else if ((match = line.match(value === undefined ? /^([^+=]+)(\+?=)(.*)/ : /^(\S[^+=]+)(\+?=)(.*)/))) {
             recordVal();
             keyPath = match[1].trim().split(/\s*\.\s*/);
@@ -110,19 +104,16 @@ function parse(text, url) {
             }
             value = match[3].trim();
         }
-        // add to existing array value
         else if (keyPath !== undefined &&
             (match = /^\s{0,4}\+\s*(.+)/.exec(line))) {
             recordVal();
             operation = '+=';
             value = match[1].trim();
         }
-        // add to existing value
         else if (value !== undefined && (match = /^\s+(\S.*)/.exec(line))) {
             const m = match[1];
             value += value.length ? ` ${m.trim()}` : m.trim();
         }
-        // done with last value
         else {
             recordVal();
             keyPath = undefined;
@@ -132,21 +123,11 @@ function parse(text, url) {
     recordVal();
     return data;
 }
-/**
- * Applies defaults and any other necessary tweaks to the loaded configuration.
- * @param conf - the object containing the configuration, which it modifies
- * in-place
- * @param url - URL of the config file
- * @returns the same object it was passed
- */
 export function regularizeConf(conf, url) {
-    // if tracks is not an array, convert it to one
     if (conf.tracks && !Array.isArray(conf.tracks)) {
-        // if it's a single track config, wrap it in an arrayref
         if (isTrack(conf.tracks)) {
             conf.tracks = [conf.tracks];
         }
-        // otherwise, coerce it to an array
         else {
             const tracks = [];
             for (const label of Object.keys(conf.tracks)) {
@@ -161,10 +142,8 @@ export function regularizeConf(conf, url) {
             conf.tracks = tracks;
         }
     }
-    // regularize trackMetadata.sources
     const meta = conf.trackMetadata;
     if (meta === null || meta === void 0 ? void 0 : meta.sources) {
-        // if it's a single source config, wrap it in an arrayref
         if (typeof meta.sources === 'string') {
             meta.sources = [meta.sources];
         }
@@ -182,7 +161,6 @@ export function regularizeConf(conf, url) {
             }
             meta.sources = sources;
         }
-        // coerce any string source defs to be URLs, and try to detect their types
         meta.sources = meta.sources.map((sourceDef) => {
             if (typeof sourceDef === 'string') {
                 const newSourceDef = { url: sourceDef };
@@ -204,8 +182,6 @@ export function regularizeConf(conf, url) {
         conf.baseUrl += '/';
     }
     if (conf.sourceUrl) {
-        // set a default baseUrl in each of the track and store confs, and the names
-        // conf, if needed
         const addBase = [];
         if (conf.tracks) {
             addBase.push(...conf.tracks);
@@ -221,7 +197,6 @@ export function regularizeConf(conf, url) {
                 t.baseUrl = conf.baseUrl || '/';
             }
         });
-        // resolve the refSeqs and nameUrl if present
         if (conf.refSeqs && typeof conf.refSeqs === 'string') {
             conf.refSeqs = new URL(conf.refSeqs, conf.sourceUrl).href;
         }
@@ -231,14 +206,11 @@ export function regularizeConf(conf, url) {
     }
     conf.stores = conf.stores || {};
     (conf.tracks || []).forEach((trackConfig) => {
-        // if there is a `config` subpart, just copy its keys in to the top-level
-        // config
         if (trackConfig.config) {
             const c = trackConfig.config;
             trackConfig.config = undefined;
             trackConfig = { ...c, ...trackConfig };
         }
-        // skip if it's a new-style track def
         if (trackConfig.store) {
             return;
         }
@@ -269,11 +241,6 @@ export function regularizeConf(conf, url) {
     });
     return conf;
 }
-/**
- * prefix class name with `root` if it contains no slashes
- * @param root - Prefix root
- * @param className - class name
- */
 function regularizeClass(root, className) {
     if (!className) {
         return '';
@@ -338,8 +305,6 @@ function guessStoreClass(trackConfig, urlTemplate) {
 }
 function synthesizeTrackStoreConfig(mainConf, trackConfig) {
     var _a;
-    // figure out what data store class to use with the track, applying some
-    // defaults if it is not explicit in the configuration
     const { urlTemplate = '' } = trackConfig;
     const storeClass = trackConfig.storeClass
         ? regularizeClass('JBrowse/Store', trackConfig.storeClass)
@@ -348,10 +313,7 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
         console.warn(`Unable to determine an appropriate data store to use with track '${trackConfig.label}', please explicitly specify a storeClass in the configuration.`);
         return;
     }
-    // synthesize a separate store conf
     const storeConf = { ...trackConfig, type: storeClass };
-    // if this is the first sequence store we see, and we have no refseqs store
-    // defined explicitly, make this the refseqs store.
     storeConf.name =
         (storeClass === 'JBrowse/Store/Sequence/StaticChunked' ||
             storeClass === 'JBrowse/Store/Sequence/IndexedFasta' ||
@@ -363,11 +325,9 @@ function synthesizeTrackStoreConfig(mainConf, trackConfig) {
             !((_a = mainConf.stores) === null || _a === void 0 ? void 0 : _a.refseqs)
             ? 'refseqs'
             : `store${objectHash(storeConf)}`;
-    // record it
     if (!mainConf.stores) {
         mainConf.stores = {};
     }
     mainConf.stores[storeConf.name] = storeConf;
-    // connect it to the track conf
     trackConfig.store = storeConf.name;
 }

package/esm/JBrowse1Connection/jb1ToJb2.d.ts

@@ -1,4 +1,4 @@
-import { Track, RefSeqs } from './types';
+import type { RefSeqs, Track } from './types';
 interface Jb2Track {
     trackId: string;
     name: string;

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -1,6 +1,6 @@
-import { openLocation } from '@jbrowse/core/util/io';
 import { objectHash } from '@jbrowse/core/util';
-import { generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, UNKNOWN, UNSUPPORTED, } from '@jbrowse/core/util/tracks';
+import { openLocation } from '@jbrowse/core/util/io';
+import { UNKNOWN, UNSUPPORTED, generateUnknownTrackConf, generateUnsupportedTrackConf, guessAdapter, guessTrackType, } from '@jbrowse/core/util/tracks';
 export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
     var _a, _b, _c, _d, _e;
     const jb2TrackConfig = {
@@ -313,8 +313,6 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             };
         }
     }
-    // If we don't recognize the store class, make a best effort to guess by file
-    // type
     jb2TrackConfig.adapter = guessAdapter({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
     if (jb2TrackConfig.adapter.type === UNSUPPORTED) {
         return generateUnsupportedTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
@@ -350,12 +348,10 @@ function generateFromConfigTrackConfig(jb1TrackConfig, jb2TrackConfig) {
 }
 export async function createRefSeqsAdapter(refSeqs) {
     if (typeof refSeqs === 'string') {
-        // assume refSeqs is a url if it is string
         refSeqs = {
             url: refSeqs,
         };
     }
-    // check refseq urls
     if (refSeqs.url) {
         if (/.fai$/.exec(refSeqs.url)) {
             return {

package/esm/JBrowse1Connection/model.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     name: import("mobx-state-tree").ISimpleType<string>;
     tracks: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
@@ -46,7 +46,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: ({
+    addTrackConf(trackConf: Record<string, unknown> | ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
@@ -56,8 +56,8 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>): any;
-    addTrackConfs(trackConfs: (({
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>)): any;
+    addTrackConfs(trackConfs: (Record<string, unknown> | ({
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
         setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
@@ -67,7 +67,7 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
                 [x: string]: any;
             } & import("mobx-state-tree/dist/internal").NonEmptyObject & any & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
         } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>);
-    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>) | Record<string, unknown>)[]): void;
+    } & import("mobx-state-tree").IStateTreeNode<import("@jbrowse/core/configuration").AnyConfigurationSchemaType>))[]): void;
     setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {

package/esm/JBrowse1Connection/model.js

@@ -1,8 +1,7 @@
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
-import { getSession } from '@jbrowse/core/util';
 import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models';
+import { getSession } from '@jbrowse/core/util';
 import { types } from 'mobx-state-tree';
-// locals
 import configSchema from './configSchema';
 export default function stateModelFactory(pluginManager) {
     return types
@@ -28,7 +27,6 @@ export default function stateModelFactory(pluginManager) {
                     throw new Error(`Assembly "${assemblyName}" not found`);
                 }
                 const sequenceAdapter = readConfObject(conf, ['sequence', 'adapter']);
-                // @ts-expect-error
                 const jb2Tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.map(jb1Track => ({
                     ...convertTrackConfig(jb1Track, config.dataRoot || '', sequenceAdapter),
                     assemblyNames: [assemblyName],

package/esm/JBrowse1Connection/util.d.ts

@@ -1,27 +1,8 @@
-import { Track, Source } from './types';
+import type { Source, Track } from './types';
 export declare function isTrack(arg: any): arg is Track;
 export declare function isSource(arg: any): arg is Source;
-/**
- * updates a with values from b, recursively
- */
 type Obj = Record<string, any>;
 export declare function deepUpdate(a: Obj, b: Obj): Obj;
-/**
- * replace variables in a template string with values
- *
- * @param template - String with variable names in curly brackets
- * e.g., `http://foo/{bar}?arg={baz.foo}`
- * @param fillWith - object with attribute-value mappings
- * e.g., `{ 'bar': 'someurl', 'baz': { 'foo': 42 } }`
- * @returns the template string with variables in fillWith replaced
- * e.g., 'htp://foo/someurl?arg=valueforbaz'
- */
 export declare function fillTemplate(template: string, fillWith: Obj): string;
-/**
- * Clones objects (including DOM nodes) and all children.
- * Warning: do not clone cyclic structures
- * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
- * @param src - The object to clone
- */
-export declare function clone(src: any): any;
+export declare function structuredClone(src: any): any;
 export {};