@jbrowse/plugin-legacy-jbrowse 2.13.0 → 2.14.0

package/dist/JBrowse1Connection/jb1ConfigLoad.js

@@ -8,9 +8,11 @@ const io_1 = require("@jbrowse/core/util/io");
 const jb1ConfigParse_1 = require("./jb1ConfigParse");
 const util_1 = require("./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;
 }
 async function fetchJb1(
@@ -111,7 +113,7 @@ function mergeConfigs(a, b) {
             const aTracks = a[prop] || [];
             const bTracks = b[prop] || [];
             if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
-                a[prop] = mergeTrackConfigs(aTracks || [], bTracks || []);
+                a[prop] = mergeTrackConfigs(aTracks, bTracks);
             }
             else {
                 throw new Error(`Track config has not been properly regularized: ${aTracks} ${bTracks}`);
@@ -181,7 +183,7 @@ async function loadIncludes(inputConfig) {
             throw new Error('Problem merging configs');
         }
         const includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
-        delete config.include;
+        config.include = undefined;
         const loads = includes.map(async (include) => {
             include.cacheBuster = inputConfig.cacheBuster;
             const includedData = await fetchConfigFile({
@@ -221,7 +223,6 @@ function regularizeIncludes(includes) {
         return include;
     });
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any,@typescript-eslint/no-unnecessary-type-constraint
 function fillTemplates(subconfig, config) {
     if (!subconfig) {
         return subconfig;
@@ -232,7 +233,6 @@ function fillTemplates(subconfig, config) {
         }
     }
     else if (typeof subconfig === 'object') {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const sub = subconfig;
         for (const name of Object.keys(sub)) {
             sub[name] = fillTemplates(sub[name], config);

package/dist/JBrowse1Connection/jb1ConfigParse.js

@@ -52,13 +52,13 @@ function parse(text, url) {
             let parsedValue;
             try {
                 // parse json
-                const match = value.match(/^json:(.+)/i);
+                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 = parseFloat(value.replaceAll(',', ''));
+                    parsedValue = Number.parseFloat(value.replaceAll(',', ''));
                 }
                 else {
                     parsedValue = value;
@@ -98,7 +98,7 @@ function parse(text, url) {
         const line = textLine.replace(/^\s*#.+/, '');
         // new section
         let match;
-        if ((match = line.match(/^\s*\[([^\]]+)/))) {
+        if ((match = /^\s*\[([^\]]+)/.exec(line))) {
             // new section
             recordVal();
             keyPath = undefined;
@@ -120,14 +120,15 @@ function parse(text, url) {
         }
         // add to existing array value
         else if (keyPath !== undefined &&
-            (match = line.match(/^\s{0,4}\+\s*(.+)/))) {
+            (match = /^\s{0,4}\+\s*(.+)/.exec(line))) {
             recordVal();
             operation = '+=';
             value = match[1].trim();
         }
         // add to existing value
-        else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
-            value += value.length ? ` ${match[1].trim()}` : match[1].trim();
+        else if (value !== undefined && (match = /^\s+(\S.*)/.exec(line))) {
+            const m = match[1];
+            value += value.length ? ` ${m.trim()}` : m.trim();
         }
         // done with last value
         else {
@@ -193,7 +194,7 @@ function regularizeConf(conf, url) {
         meta.sources = meta.sources.map((sourceDef) => {
             if (typeof sourceDef === 'string') {
                 const newSourceDef = { url: sourceDef };
-                const typeMatch = sourceDef.match(/\.(\w+)$/);
+                const typeMatch = /\.(\w+)$/.exec(sourceDef);
                 if (typeMatch) {
                     newSourceDef.type = typeMatch[1].toLowerCase();
                 }
@@ -242,7 +243,7 @@ function regularizeConf(conf, url) {
         // config
         if (trackConfig.config) {
             const c = trackConfig.config;
-            delete trackConfig.config;
+            trackConfig.config = undefined;
             trackConfig = { ...c, ...trackConfig };
         }
         // skip if it's a new-style track def

package/dist/JBrowse1Connection/jb1ToJb2.js

@@ -317,11 +317,9 @@ function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             };
         }
     }
-    // If we don't recognize the store class, make a best effort to guess by file type
+    // If we don't recognize the store class, make a best effort to guess by file
+    // type
     jb2TrackConfig.adapter = (0, tracks_1.guessAdapter)({ uri: urlTemplate, locationType: 'UriLocation' }, undefined, urlTemplate);
-    if (!jb2TrackConfig.adapter) {
-        throw new Error('Could not determine adapter');
-    }
     if (jb2TrackConfig.adapter.type === tracks_1.UNSUPPORTED) {
         return (0, tracks_1.generateUnsupportedTrackConf)(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
     }
@@ -363,7 +361,7 @@ async function createRefSeqsAdapter(refSeqs) {
     }
     // check refseq urls
     if (refSeqs.url) {
-        if (refSeqs.url.match(/.fai$/)) {
+        if (/.fai$/.exec(refSeqs.url)) {
             return {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: {
@@ -376,16 +374,16 @@ async function createRefSeqsAdapter(refSeqs) {
                 },
             };
         }
-        if (refSeqs.url.match(/.2bit$/)) {
+        if (/.2bit$/.exec(refSeqs.url)) {
             return {
                 type: 'TwoBitAdapter',
                 twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
             };
         }
-        if (refSeqs.url.match(/.fa$/)) {
+        if (/.fa$/.exec(refSeqs.url)) {
             throw new Error('Unindexed FASTA adapter not available');
         }
-        if (refSeqs.url.match(/.sizes/)) {
+        if (/.sizes/.exec(refSeqs.url)) {
             throw new Error('chromosome SIZES adapter not available');
         }
         const refSeqsJson = await (0, io_1.openLocation)({

package/dist/JBrowse1Connection/model.d.ts

@@ -46,9 +46,29 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
-    addTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): any[];
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
+    addTrackConf(trackConf: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [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: (({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [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;
+    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
     connect(): Promise<void>;

package/dist/JBrowse1Connection/util.js

@@ -9,11 +9,9 @@ exports.deepUpdate = deepUpdate;
 exports.fillTemplate = fillTemplate;
 exports.clone = clone;
 const get_value_1 = __importDefault(require("get-value"));
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isTrack(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isSource(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
 }
@@ -63,7 +61,6 @@ function fillTemplate(template, fillWith) {
  * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
  * @param src - The object to clone
  */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 function clone(src) {
     if (!src ||
         typeof src !== 'object' ||
@@ -84,12 +81,10 @@ function clone(src) {
         return new RegExp(src); // RegExp
     }
     let r;
-    let i;
-    let l;
     if (Array.isArray(src)) {
         // array
         r = [];
-        for (i = 0, l = src.length; i < l; ++i) {
+        for (let i = 0, l = src.length; i < l; ++i) {
             if (i in src) {
                 r[i] = clone(src[i]);
             }
@@ -123,15 +118,13 @@ function clone(src) {
  * @returns dest, as modified
  */
 function mixin(dest, source, copyFunc) {
-    let name;
-    let s;
     const empty = {};
-    for (name in source) {
+    for (const name in source) {
         // the (!(name in empty) || empty[name] !== s) condition avoids copying
         // properties in "source" inherited from Object.prototype.	 For example,
         // if dest has a custom toString() method, don't overwrite it with the
         // toString() method that source inherited from Object.prototype
-        s = source[name];
+        const s = source[name];
         if (!(name in dest) ||
             // @ts-expect-error
             (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {

package/dist/JBrowse1TextSearchAdapter/HttpMap.js

@@ -7,7 +7,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */
-const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
+const crc32_1 = __importDefault(require("crc/crc32"));
 class HttpMap {
     constructor(args) {
         // make sure url has a trailing slash
@@ -85,10 +85,7 @@ class HttpMap {
         return '';
     }
     hash(data) {
-        return (0, buffer_crc32_1.default)(Buffer.from(data))
-            .toString('hex')
-            .toLowerCase()
-            .replace('-', 'n');
+        return (0, crc32_1.default)(Buffer.from(data)).toString(16).toLowerCase().replace('-', 'n');
     }
 }
 exports.default = HttpMap;

package/dist/NCListAdapter/NCListAdapter.js

@@ -41,7 +41,6 @@ class NCListAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     wrapFeature(ncFeature) {
         return new NCListFeature_1.default(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
     }

package/dist/NCListAdapter/NCListFeature.js

@@ -6,9 +6,7 @@ const jb1ToJb2 = { seq_id: 'refName' };
  * wrapper to adapt nclist features to act like jbrowse 2 features
  */
 class NCListFeature {
-    constructor(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    ncFeature, parent, id) {
+    constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();
         this.parentHandle = parent;
@@ -26,11 +24,9 @@ class NCListFeature {
         // @ts-expect-error
         return jb1ToJb2[t] || t;
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(attrName) {
         const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
         if (attr && attrName === 'subfeatures') {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return attr.map((subfeature) => new NCListFeature(subfeature, this));
         }
         return attr;

package/esm/JBrowse1Connection/jb1ConfigLoad.js

@@ -2,9 +2,11 @@ import { openLocation } from '@jbrowse/core/util/io';
 import { parseJB1Json, parseJB1Conf, regularizeConf } from './jb1ConfigParse';
 import { clone, 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(
@@ -105,7 +107,7 @@ function mergeConfigs(a, b) {
             const aTracks = a[prop] || [];
             const bTracks = b[prop] || [];
             if (Array.isArray(aTracks) && Array.isArray(bTracks)) {
-                a[prop] = mergeTrackConfigs(aTracks || [], bTracks || []);
+                a[prop] = mergeTrackConfigs(aTracks, bTracks);
             }
             else {
                 throw new Error(`Track config has not been properly regularized: ${aTracks} ${bTracks}`);
@@ -175,7 +177,7 @@ async function loadIncludes(inputConfig) {
             throw new Error('Problem merging configs');
         }
         const includes = fillTemplates(regularizeIncludes(config.include || []), newUpstreamConf);
-        delete config.include;
+        config.include = undefined;
         const loads = includes.map(async (include) => {
             include.cacheBuster = inputConfig.cacheBuster;
             const includedData = await fetchConfigFile({
@@ -215,7 +217,6 @@ function regularizeIncludes(includes) {
         return include;
     });
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any,@typescript-eslint/no-unnecessary-type-constraint
 function fillTemplates(subconfig, config) {
     if (!subconfig) {
         return subconfig;
@@ -226,7 +227,6 @@ function fillTemplates(subconfig, config) {
         }
     }
     else if (typeof subconfig === 'object') {
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
         const sub = subconfig;
         for (const name of Object.keys(sub)) {
             sub[name] = fillTemplates(sub[name], config);

package/esm/JBrowse1Connection/jb1ConfigParse.js

@@ -44,13 +44,13 @@ function parse(text, url) {
             let parsedValue;
             try {
                 // parse json
-                const match = value.match(/^json:(.+)/i);
+                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 = parseFloat(value.replaceAll(',', ''));
+                    parsedValue = Number.parseFloat(value.replaceAll(',', ''));
                 }
                 else {
                     parsedValue = value;
@@ -90,7 +90,7 @@ function parse(text, url) {
         const line = textLine.replace(/^\s*#.+/, '');
         // new section
         let match;
-        if ((match = line.match(/^\s*\[([^\]]+)/))) {
+        if ((match = /^\s*\[([^\]]+)/.exec(line))) {
             // new section
             recordVal();
             keyPath = undefined;
@@ -112,14 +112,15 @@ function parse(text, url) {
         }
         // add to existing array value
         else if (keyPath !== undefined &&
-            (match = line.match(/^\s{0,4}\+\s*(.+)/))) {
+            (match = /^\s{0,4}\+\s*(.+)/.exec(line))) {
             recordVal();
             operation = '+=';
             value = match[1].trim();
         }
         // add to existing value
-        else if (value !== undefined && (match = line.match(/^\s+(\S.*)/))) {
-            value += value.length ? ` ${match[1].trim()}` : match[1].trim();
+        else if (value !== undefined && (match = /^\s+(\S.*)/.exec(line))) {
+            const m = match[1];
+            value += value.length ? ` ${m.trim()}` : m.trim();
         }
         // done with last value
         else {
@@ -185,7 +186,7 @@ export function regularizeConf(conf, url) {
         meta.sources = meta.sources.map((sourceDef) => {
             if (typeof sourceDef === 'string') {
                 const newSourceDef = { url: sourceDef };
-                const typeMatch = sourceDef.match(/\.(\w+)$/);
+                const typeMatch = /\.(\w+)$/.exec(sourceDef);
                 if (typeMatch) {
                     newSourceDef.type = typeMatch[1].toLowerCase();
                 }
@@ -234,7 +235,7 @@ export function regularizeConf(conf, url) {
         // config
         if (trackConfig.config) {
             const c = trackConfig.config;
-            delete trackConfig.config;
+            trackConfig.config = undefined;
             trackConfig = { ...c, ...trackConfig };
         }
         // skip if it's a new-style track def

package/esm/JBrowse1Connection/jb1ToJb2.js

@@ -313,11 +313,9 @@ export function convertTrackConfig(jb1TrackConfig, dataRoot, sequenceAdapter) {
             };
         }
     }
-    // If we don't recognize the store class, make a best effort to guess by file type
+    // 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) {
-        throw new Error('Could not determine adapter');
-    }
     if (jb2TrackConfig.adapter.type === UNSUPPORTED) {
         return generateUnsupportedTrackConf(jb2TrackConfig.name, urlTemplate, jb2TrackConfig.category);
     }
@@ -359,7 +357,7 @@ export async function createRefSeqsAdapter(refSeqs) {
     }
     // check refseq urls
     if (refSeqs.url) {
-        if (refSeqs.url.match(/.fai$/)) {
+        if (/.fai$/.exec(refSeqs.url)) {
             return {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: {
@@ -372,16 +370,16 @@ export async function createRefSeqsAdapter(refSeqs) {
                 },
             };
         }
-        if (refSeqs.url.match(/.2bit$/)) {
+        if (/.2bit$/.exec(refSeqs.url)) {
             return {
                 type: 'TwoBitAdapter',
                 twoBitLocation: { uri: refSeqs.url, locationType: 'UriLocation' },
             };
         }
-        if (refSeqs.url.match(/.fa$/)) {
+        if (/.fa$/.exec(refSeqs.url)) {
             throw new Error('Unindexed FASTA adapter not available');
         }
-        if (refSeqs.url.match(/.sizes/)) {
+        if (/.sizes/.exec(refSeqs.url)) {
             throw new Error('chromosome SIZES adapter not available');
         }
         const refSeqsJson = await openLocation({

package/esm/JBrowse1Connection/model.d.ts

@@ -46,9 +46,29 @@ export default function stateModelFactory(pluginManager: PluginManager): import(
     connect(_arg: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
 } & {
     afterAttach(): void;
-    addTrackConf(trackConf: import("@jbrowse/core/configuration").AnyConfigurationModel): any;
-    addTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): any[];
-    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): import("mobx-state-tree").IMSTArray<import("mobx-state-tree").IAnyModelType> & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>>;
+    addTrackConf(trackConf: ({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [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: (({
+        [x: string]: any;
+    } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+        setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+            [x: string]: any;
+        } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
+            setSubschema(slotName: string, data: Record<string, unknown>): Record<string, unknown> | ({
+                [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;
+    setTrackConfs(trackConfs: import("@jbrowse/core/configuration").AnyConfigurationModel[]): void;
     clear(): void;
 } & {
     connect(): Promise<void>;

package/esm/JBrowse1Connection/util.js

@@ -1,9 +1,7 @@
 import getValue from 'get-value';
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function isTrack(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.label) && typeof arg.label === 'string';
 }
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function isSource(arg) {
     return (arg === null || arg === void 0 ? void 0 : arg.url) && typeof arg.url === 'string';
 }
@@ -53,7 +51,6 @@ export function fillTemplate(template, fillWith) {
  * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
  * @param src - The object to clone
  */
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function clone(src) {
     if (!src ||
         typeof src !== 'object' ||
@@ -74,12 +71,10 @@ export function clone(src) {
         return new RegExp(src); // RegExp
     }
     let r;
-    let i;
-    let l;
     if (Array.isArray(src)) {
         // array
         r = [];
-        for (i = 0, l = src.length; i < l; ++i) {
+        for (let i = 0, l = src.length; i < l; ++i) {
             if (i in src) {
                 r[i] = clone(src[i]);
             }
@@ -113,15 +108,13 @@ export function clone(src) {
  * @returns dest, as modified
  */
 function mixin(dest, source, copyFunc) {
-    let name;
-    let s;
     const empty = {};
-    for (name in source) {
+    for (const name in source) {
         // the (!(name in empty) || empty[name] !== s) condition avoids copying
         // properties in "source" inherited from Object.prototype.	 For example,
         // if dest has a custom toString() method, don't overwrite it with the
         // toString() method that source inherited from Object.prototype
-        s = source[name];
+        const s = source[name];
         if (!(name in dest) ||
             // @ts-expect-error
             (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {

package/esm/JBrowse1TextSearchAdapter/HttpMap.js

@@ -2,7 +2,7 @@
  * Helper class allows reading names index generated in JBrowse1
  * Adapted from https://github.com/GMOD/jbrowse/blob/master/src/JBrowse/Store/Hash.js
  */
-import crc32 from 'buffer-crc32';
+import crc32 from 'crc/crc32';
 export default class HttpMap {
     constructor(args) {
         // make sure url has a trailing slash
@@ -80,9 +80,6 @@ export default class HttpMap {
         return '';
     }
     hash(data) {
-        return crc32(Buffer.from(data))
-            .toString('hex')
-            .toLowerCase()
-            .replace('-', 'n');
+        return crc32(Buffer.from(data)).toString(16).toLowerCase().replace('-', 'n');
     }
 }

package/esm/NCListAdapter/NCListAdapter.js

@@ -36,7 +36,6 @@ export default class NCListAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         });
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     wrapFeature(ncFeature) {
         return new NCListFeature(ncFeature, undefined, `${this.id}-${ncFeature.id()}`);
     }

package/esm/NCListAdapter/NCListFeature.js

@@ -4,9 +4,7 @@ const jb1ToJb2 = { seq_id: 'refName' };
  * wrapper to adapt nclist features to act like jbrowse 2 features
  */
 export default class NCListFeature {
-    constructor(
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    ncFeature, parent, id) {
+    constructor(ncFeature, parent, id) {
         this.ncFeature = ncFeature;
         this.uniqueId = id || ncFeature.id();
         this.parentHandle = parent;
@@ -24,11 +22,9 @@ export default class NCListFeature {
         // @ts-expect-error
         return jb1ToJb2[t] || t;
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     get(attrName) {
         const attr = this.ncFeature.get(this.jb2TagToJb1Tag(attrName));
         if (attr && attrName === 'subfeatures') {
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
             return attr.map((subfeature) => new NCListFeature(subfeature, this));
         }
         return attr;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-legacy-jbrowse",
-  "version": "2.13.0",
+  "version": "2.14.0",
   "description": "JBrowse 2 plugin for connecting to and reading JBrowse 1 data",
   "keywords": [
     "jbrowse",
@@ -24,7 +24,7 @@
   ],
   "scripts": {
     "build": "npm-run-all build:*",
-    "test": "cd ../..; jest plugins/legacy-jbrowse",
+    "test": "cd ../..; jest --passWithNoTests plugins/legacy-jbrowse",
     "prepublishOnly": "yarn test",
     "prepack": "yarn build && yarn useDist",
     "postpack": "yarn useSrc",
@@ -37,7 +37,7 @@
   },
   "dependencies": {
     "@gmod/nclist": "^1.0.3",
-    "buffer-crc32": "^1.0.0",
+    "crc": "^4.0.0",
     "generic-filehandle": "^3.0.0",
     "get-value": "^3.0.1",
     "set-value": "^4.0.1"
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "efe02fb9616e20e929cceeed46eb96420c1b6923"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }