@jbrowse/cli 4.0.4 → 4.1.3

package/dist/base.js

@@ -1,5 +1,4 @@
-"use strict";
 /**
  * By convention, exit codes in this base class are below 100
  */
-Object.defineProperty(exports, "__esModule", { value: true });
+export {};

package/dist/bin.js

@@ -1,7 +1,5 @@
 #!/usr/bin/env node
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const index_ts_1 = require("./index.js");
-(0, index_ts_1.main)(process.argv.slice(2)).catch((e) => {
+import { main } from "./index.js";
+main(process.argv.slice(2)).catch((e) => {
     console.error(e);
 });

package/dist/cliFetch.js

@@ -0,0 +1,3 @@
+export default function cliFetch(url, options = {}) {
+    return fetch(url, options);
+}

package/dist/commands/add-assembly/index.js

@@ -1,15 +1,12 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const utils_ts_1 = require("./utils.js");
-const utils_ts_2 = require("../../utils.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { addAssemblyToConfig, enhanceAssembly, getAssembly, loadOrCreateConfig, resolveTargetPath, saveConfigAndReport, } from "./utils.js";
+import { debug, printHelp } from "../../utils.js";
+export async function run(args) {
     const options = {
         type: {
             type: 'string',
             short: 't',
-            description: `type of sequence, by default inferred from sequence file\n\nindexedFasta   An index FASTA (e.g. .fa or .fasta) file;\n               can optionally specify --faiLocation\n\nbgzipFasta     A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file;\n               can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit         A twoBit (e.g. .2bit) file\n\nchromSizes     A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom         Either a JSON file location or inline JSON that defines a custom\n               sequence adapter; must provide --name if using inline JSON`,
+            description: `type of sequence, by default inferred from sequence file\n\nindexedFasta - An index FASTA (e.g. .fa or .fasta) file; can optionally specify --faiLocation\n\nbgzipFasta - A block-gzipped and indexed FASTA (e.g. .fa.gz or .fasta.gz) file; can optionally specify --faiLocation and/or --gziLocation\n\ntwoBit - A twoBit (e.g. .2bit) file\n\nchromSizes - A chromosome sizes (e.g. .chrom.sizes) file\n\ncustom - Either a JSON file location or inline JSON that defines a custom sequence adapter; must provide --name if using inline JSON`,
             choices: ['indexedFasta', 'bgzipFasta', 'twoBit', 'chromSizes', 'custom'],
         },
         name: {
@@ -20,7 +17,7 @@ async function run(args) {
         alias: {
             type: 'string',
             short: 'a',
-            description: 'An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38");\ncan be specified multiple times',
+            description: 'An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38"); can be specified multiple times',
             multiple: true,
         },
         displayName: {
@@ -37,21 +34,21 @@ async function run(args) {
         },
         refNameAliases: {
             type: 'string',
-            description: 'Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified',
+            description: 'Reference sequence name aliases file or URL; assumed to be a tab-separated aliases file unless --refNameAliasesType is specified',
         },
         refNameAliasesType: {
             type: 'string',
-            description: 'Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter',
+            description: 'Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either a JSON file location or inline JSON that defines a custom sequence adapter',
             choices: ['aliases', 'custom'],
             dependsOn: ['refNameAliases'],
         },
         refNameColors: {
             type: 'string',
-            description: 'A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences',
+            description: 'A comma-separated list of color strings for the reference sequence names; will cycle through colors if there are fewer colors than sequences',
         },
         target: {
             type: 'string',
-            description: 'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',
+            description: 'path to config file in JB2 installation directory to write out to. Creates ./config.json if nonexistent',
         },
         out: {
             type: 'string',
@@ -82,7 +79,7 @@ async function run(args) {
             description: 'Equivalent to `--skipCheck --overwrite`',
         },
     };
-    const { positionals, values: runFlags } = (0, util_1.parseArgs)({
+    const { positionals, values: runFlags } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -114,7 +111,7 @@ async function run(args) {
         '$ jbrowse add-assembly myfile.fa.gz --load copy',
     ];
     if (runFlags.help) {
-        (0, utils_ts_2.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse add-assembly <sequence> [options]',
@@ -124,17 +121,17 @@ async function run(args) {
     }
     const argsSequence = positionals[0] || '';
     const output = runFlags.target || runFlags.out || '.';
-    (0, utils_ts_2.debug)(`Sequence location is: ${argsSequence}`);
-    const target = await (0, utils_ts_1.resolveTargetPath)(output);
-    const baseAssembly = await (0, utils_ts_1.getAssembly)({ runFlags, argsSequence, target });
-    const assembly = await (0, utils_ts_1.enhanceAssembly)(baseAssembly, runFlags);
-    const configContents = await (0, utils_ts_1.loadOrCreateConfig)(target);
-    const { config: updatedConfig, wasOverwritten } = await (0, utils_ts_1.addAssemblyToConfig)({
+    debug(`Sequence location is: ${argsSequence}`);
+    const target = await resolveTargetPath(output);
+    const baseAssembly = await getAssembly({ runFlags, argsSequence, target });
+    const assembly = await enhanceAssembly(baseAssembly, runFlags);
+    const configContents = await loadOrCreateConfig(target);
+    const { config: updatedConfig, wasOverwritten } = await addAssemblyToConfig({
         config: configContents,
         assembly,
         runFlags,
     });
-    await (0, utils_ts_1.saveConfigAndReport)({
+    await saveConfigAndReport({
         config: updatedConfig,
         target,
         assembly,

package/dist/commands/add-assembly/utils.js

@@ -1,27 +1,10 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isValidJSON = isValidJSON;
-exports.guessSequenceType = guessSequenceType;
-exports.needLoadData = needLoadData;
-exports.loadData = loadData;
-exports.getAssembly = getAssembly;
-exports.exists = exists;
-exports.resolveTargetPath = resolveTargetPath;
-exports.enhanceAssembly = enhanceAssembly;
-exports.createDefaultConfig = createDefaultConfig;
-exports.loadOrCreateConfig = loadOrCreateConfig;
-exports.addAssemblyToConfig = addAssemblyToConfig;
-exports.saveConfigAndReport = saveConfigAndReport;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const common_ts_1 = require("../../types/common.js");
-const utils_ts_1 = require("../../utils.js");
-const config_operations_ts_1 = require("../shared/config-operations.js");
-const { rename, copyFile, symlink } = fs_1.default.promises;
-function isValidJSON(string) {
+import fs from 'fs';
+import path from 'path';
+import { isURL } from "../../types/common.js";
+import { debug, readInlineOrFileJson, readJsonFile, resolveFileLocation, } from "../../utils.js";
+import { findAndUpdateOrAdd, saveConfigAndReport as saveConfigAndReportBase, } from "../shared/config-operations.js";
+const { rename, copyFile, symlink } = fs.promises;
+export function isValidJSON(string) {
     try {
         JSON.parse(string);
         return true;
@@ -30,7 +13,7 @@ function isValidJSON(string) {
         return false;
     }
 }
-function guessSequenceType(sequence) {
+export function guessSequenceType(sequence) {
     if (sequence.endsWith('.fa') ||
         sequence.endsWith('.fna') ||
         sequence.endsWith('.fasta')) {
@@ -55,31 +38,31 @@ function guessSequenceType(sequence) {
     }
     throw new Error('Could not determine sequence type automatically, add --type to specify it');
 }
-function needLoadData(location) {
-    return !(0, common_ts_1.isURL)(location);
+export function needLoadData(location) {
+    return !isURL(location);
 }
-async function loadData({ load, filePaths, destination, }) {
-    if ((0, common_ts_1.isURL)(filePaths[0])) {
+export async function loadData({ load, filePaths, destination, }) {
+    if (isURL(filePaths[0])) {
         return false;
     }
     if (load === 'inPlace') {
         return false;
     }
-    const destDir = path_1.default.dirname(destination);
+    const destDir = path.dirname(destination);
     const validPaths = filePaths.filter(f => !!f);
     const operations = {
         copy: copyFile,
-        symlink: (src, dest) => symlink(path_1.default.resolve(src), dest),
+        symlink: (src, dest) => symlink(path.resolve(src), dest),
         move: rename,
     };
     const operation = operations[load];
     if (operation) {
-        await Promise.all(validPaths.map(filePath => operation(filePath, path_1.default.join(destDir, path_1.default.basename(filePath)))));
+        await Promise.all(validPaths.map(filePath => operation(filePath, path.join(destDir, path.basename(filePath)))));
         return true;
     }
     return false;
 }
-async function getAssembly({ runFlags, argsSequence, target, }) {
+export async function getAssembly({ runFlags, argsSequence, target, }) {
     let sequence;
     if (needLoadData(argsSequence) && !runFlags.load) {
         throw new Error('Please specify the loading operation for this file with --load copy|symlink|move|inPlace');
@@ -90,25 +73,25 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
     let { name } = runFlags;
     let { type } = runFlags;
     if (type) {
-        (0, utils_ts_1.debug)(`Type is: ${type}`);
+        debug(`Type is: ${type}`);
     }
     else {
         type = guessSequenceType(argsSequence);
-        (0, utils_ts_1.debug)(`No type specified, guessing type: ${type}`);
+        debug(`No type specified, guessing type: ${type}`);
     }
     if (name) {
-        (0, utils_ts_1.debug)(`Name is: ${name}`);
+        debug(`Name is: ${name}`);
     }
     switch (type) {
         case 'indexedFasta': {
             const { skipCheck, force, load, faiLocation } = runFlags;
-            let sequenceLocation = await (0, utils_ts_1.resolveFileLocation)(argsSequence, !(skipCheck || force), load === 'inPlace');
-            (0, utils_ts_1.debug)(`FASTA location resolved to: ${sequenceLocation}`);
-            let indexLocation = await (0, utils_ts_1.resolveFileLocation)(faiLocation || `${argsSequence}.fai`, !(skipCheck || force), load === 'inPlace');
-            (0, utils_ts_1.debug)(`FASTA index location resolved to: ${indexLocation}`);
+            let sequenceLocation = await resolveFileLocation(argsSequence, !(skipCheck || force), load === 'inPlace');
+            debug(`FASTA location resolved to: ${sequenceLocation}`);
+            let indexLocation = await resolveFileLocation(faiLocation || `${argsSequence}.fai`, !(skipCheck || force), load === 'inPlace');
+            debug(`FASTA index location resolved to: ${indexLocation}`);
             if (!name) {
-                name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta') ? '.fasta' : '.fa');
-                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
+                name = path.basename(sequenceLocation, sequenceLocation.endsWith('.fasta') ? '.fasta' : '.fa');
+                debug(`Guessing name: ${name}`);
             }
             const loaded = load
                 ? await loadData({
@@ -118,8 +101,8 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
                 })
                 : false;
             if (loaded) {
-                sequenceLocation = path_1.default.basename(sequenceLocation);
-                indexLocation = path_1.default.basename(indexLocation);
+                sequenceLocation = path.basename(sequenceLocation);
+                indexLocation = path.basename(indexLocation);
             }
             sequence = {
                 type: 'ReferenceSequenceTrack',
@@ -136,15 +119,15 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'bgzipFasta': {
-            let sequenceLocation = await (0, utils_ts_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`compressed FASTA location resolved to: ${sequenceLocation}`);
-            let indexLocation = await (0, utils_ts_1.resolveFileLocation)(runFlags.faiLocation || `${sequenceLocation}.fai`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`compressed FASTA index location resolved to: ${indexLocation}`);
-            let bgzipIndexLocation = await (0, utils_ts_1.resolveFileLocation)(runFlags.gziLocation || `${sequenceLocation}.gzi`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`bgzip index location resolved to: ${bgzipIndexLocation}`);
+            let sequenceLocation = await resolveFileLocation(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`compressed FASTA location resolved to: ${sequenceLocation}`);
+            let indexLocation = await resolveFileLocation(runFlags.faiLocation || `${sequenceLocation}.fai`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`compressed FASTA index location resolved to: ${indexLocation}`);
+            let bgzipIndexLocation = await resolveFileLocation(runFlags.gziLocation || `${sequenceLocation}.gzi`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`bgzip index location resolved to: ${bgzipIndexLocation}`);
             if (!name) {
-                name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta.gz') ? '.fasta.gz' : '.fa.gz');
-                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
+                name = path.basename(sequenceLocation, sequenceLocation.endsWith('.fasta.gz') ? '.fasta.gz' : '.fa.gz');
+                debug(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -154,9 +137,9 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
                 })
                 : false;
             if (loaded) {
-                sequenceLocation = path_1.default.basename(sequenceLocation);
-                indexLocation = path_1.default.basename(indexLocation);
-                bgzipIndexLocation = path_1.default.basename(bgzipIndexLocation);
+                sequenceLocation = path.basename(sequenceLocation);
+                indexLocation = path.basename(indexLocation);
+                bgzipIndexLocation = path.basename(bgzipIndexLocation);
             }
             sequence = {
                 type: 'ReferenceSequenceTrack',
@@ -177,11 +160,11 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'twoBit': {
-            let sequenceLocation = await (0, utils_ts_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`2bit location resolved to: ${sequenceLocation}`);
+            let sequenceLocation = await resolveFileLocation(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`2bit location resolved to: ${sequenceLocation}`);
             if (!name) {
-                name = path_1.default.basename(sequenceLocation, '.2bit');
-                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
+                name = path.basename(sequenceLocation, '.2bit');
+                debug(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -191,7 +174,7 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
                 })
                 : false;
             if (loaded) {
-                sequenceLocation = path_1.default.basename(sequenceLocation);
+                sequenceLocation = path.basename(sequenceLocation);
             }
             sequence = {
                 type: 'ReferenceSequenceTrack',
@@ -207,11 +190,11 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'chromSizes': {
-            let sequenceLocation = await (0, utils_ts_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`chrom.sizes location resolved to: ${sequenceLocation}`);
+            let sequenceLocation = await resolveFileLocation(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`chrom.sizes location resolved to: ${sequenceLocation}`);
             if (!name) {
-                name = path_1.default.basename(sequenceLocation, '.chrom.sizes');
-                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
+                name = path.basename(sequenceLocation, '.chrom.sizes');
+                debug(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -221,7 +204,7 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
                 })
                 : false;
             if (loaded) {
-                sequenceLocation = path_1.default.basename(sequenceLocation);
+                sequenceLocation = path.basename(sequenceLocation);
             }
             sequence = {
                 type: 'ReferenceSequenceTrack',
@@ -237,16 +220,16 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'custom': {
-            const adapter = await (0, utils_ts_1.readInlineOrFileJson)(argsSequence);
-            (0, utils_ts_1.debug)(`Custom adapter: ${JSON.stringify(adapter)}`);
+            const adapter = await readInlineOrFileJson(argsSequence);
+            debug(`Custom adapter: ${JSON.stringify(adapter)}`);
             if (!name) {
                 if (isValidJSON(argsSequence)) {
                     throw new Error('Must provide --name when using custom inline JSON sequence');
                 }
                 else {
-                    name = path_1.default.basename(argsSequence, '.json');
+                    name = path.basename(argsSequence, '.json');
                 }
-                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
+                debug(`Guessing name: ${name}`);
             }
             if (!('type' in adapter)) {
                 throw new Error(`No "type" specified in sequence adapter "${JSON.stringify(adapter)}"`);
@@ -261,31 +244,31 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
     }
     return { name, sequence };
 }
-async function exists(s) {
+export async function exists(s) {
     try {
-        await fs_1.default.promises.access(s, fs_1.default.constants.F_OK);
+        await fs.promises.access(s, fs.constants.F_OK);
         return true;
     }
     catch {
         return false;
     }
 }
-async function resolveTargetPath(output) {
+export async function resolveTargetPath(output) {
     if (!(await exists(output))) {
-        const dir = output.endsWith('.json') ? path_1.default.dirname(output) : output;
-        await fs_1.default.promises.mkdir(dir, { recursive: true });
+        const dir = output.endsWith('.json') ? path.dirname(output) : output;
+        await fs.promises.mkdir(dir, { recursive: true });
     }
     let isDir = false;
     try {
-        isDir = fs_1.default.statSync(output).isDirectory();
+        isDir = fs.statSync(output).isDirectory();
     }
     catch (e) { }
-    return isDir ? path_1.default.join(output, 'config.json') : output;
+    return isDir ? path.join(output, 'config.json') : output;
 }
-async function enhanceAssembly(assembly, runFlags) {
+export async function enhanceAssembly(assembly, runFlags) {
     const enhancedAssembly = { ...assembly };
     if (runFlags.alias?.length) {
-        (0, utils_ts_1.debug)(`Adding assembly aliases: ${runFlags.alias}`);
+        debug(`Adding assembly aliases: ${runFlags.alias}`);
         enhancedAssembly.aliases = runFlags.alias;
     }
     if (runFlags.refNameColors) {
@@ -296,18 +279,18 @@ async function enhanceAssembly(assembly, runFlags) {
     if (runFlags.refNameAliases) {
         if (runFlags.refNameAliasesType &&
             runFlags.refNameAliasesType === 'custom') {
-            const refNameAliasesConfig = await (0, utils_ts_1.readInlineOrFileJson)(runFlags.refNameAliases);
+            const refNameAliasesConfig = await readInlineOrFileJson(runFlags.refNameAliases);
             if (!refNameAliasesConfig.type) {
                 throw new Error(`No "type" specified in refNameAliases adapter "${JSON.stringify(refNameAliasesConfig)}"`);
             }
-            (0, utils_ts_1.debug)(`Adding custom refNameAliases config: ${JSON.stringify(refNameAliasesConfig)}`);
+            debug(`Adding custom refNameAliases config: ${JSON.stringify(refNameAliasesConfig)}`);
             enhancedAssembly.refNameAliases = {
                 adapter: refNameAliasesConfig,
             };
         }
         else {
-            const refNameAliasesLocation = await (0, utils_ts_1.resolveFileLocation)(runFlags.refNameAliases, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_ts_1.debug)(`refName aliases file location resolved to: ${refNameAliasesLocation}`);
+            const refNameAliasesLocation = await resolveFileLocation(runFlags.refNameAliases, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
+            debug(`refName aliases file location resolved to: ${refNameAliasesLocation}`);
             enhancedAssembly.refNameAliases = {
                 adapter: {
                     type: 'RefNameAliasAdapter',
@@ -324,7 +307,7 @@ async function enhanceAssembly(assembly, runFlags) {
     }
     return enhancedAssembly;
 }
-function createDefaultConfig() {
+export function createDefaultConfig() {
     return {
         assemblies: [],
         configuration: {},
@@ -335,22 +318,22 @@ function createDefaultConfig() {
         tracks: [],
     };
 }
-async function loadOrCreateConfig(target) {
+export async function loadOrCreateConfig(target) {
     const defaultConfig = createDefaultConfig();
-    if (fs_1.default.existsSync(target)) {
-        (0, utils_ts_1.debug)(`Found existing config file ${target}`);
+    if (fs.existsSync(target)) {
+        debug(`Found existing config file ${target}`);
         return {
             ...defaultConfig,
-            ...(await (0, utils_ts_1.readJsonFile)(target)),
+            ...(await readJsonFile(target)),
         };
     }
     else {
-        (0, utils_ts_1.debug)(`Creating config file ${target}`);
+        debug(`Creating config file ${target}`);
         return { ...defaultConfig };
     }
 }
-async function addAssemblyToConfig({ config, assembly, runFlags, }) {
-    const { updatedItems, wasOverwritten } = (0, config_operations_ts_1.findAndUpdateOrAdd)({
+export async function addAssemblyToConfig({ config, assembly, runFlags, }) {
+    const { updatedItems, wasOverwritten } = findAndUpdateOrAdd({
         items: config.assemblies || [],
         newItem: assembly,
         idField: 'name',
@@ -363,8 +346,8 @@ async function addAssemblyToConfig({ config, assembly, runFlags, }) {
         wasOverwritten,
     };
 }
-async function saveConfigAndReport({ config, target, assembly, wasOverwritten, }) {
-    await (0, config_operations_ts_1.saveConfigAndReport)({
+export async function saveConfigAndReport({ config, target, assembly, wasOverwritten, }) {
+    await saveConfigAndReportBase({
         config,
         target,
         itemType: 'assembly',

package/dist/commands/add-connection.js

@@ -1,14 +1,8 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const path_1 = __importDefault(require("path"));
-const util_1 = require("util");
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const fetchWithProxy_ts_1 = __importDefault(require("../fetchWithProxy.js"));
-const utils_ts_1 = require("../utils.js");
+import path from 'path';
+import { parseArgs } from 'util';
+import parseJSON from 'json-parse-better-errors';
+import fetch from "../cliFetch.js";
+import { debug, printHelp, readJsonFile, resolveConfigPath, writeJsonFile, } from "../utils.js";
 async function resolveURL(location, check = true) {
     let locationUrl;
     try {
@@ -18,7 +12,7 @@ async function resolveURL(location, check = true) {
         throw new Error(`The location ${location} provided is not a valid URL`);
     }
     if (check) {
-        const response = await (0, fetchWithProxy_ts_1.default)(`${locationUrl}`, { method: 'HEAD' });
+        const response = await fetch(`${locationUrl}`, { method: 'HEAD' });
         if (!response.ok) {
             throw new Error(`HTTP ${response.status} fetching ${locationUrl}`);
         }
@@ -26,7 +20,7 @@ async function resolveURL(location, check = true) {
     return locationUrl.href;
 }
 function determineConnectionType(url) {
-    if (path_1.default.basename(url) === 'hub.txt') {
+    if (path.basename(url) === 'hub.txt') {
         return 'UCSCTrackHubConnection';
     }
     if (url.includes('jbrowse/data')) {
@@ -34,7 +28,7 @@ function determineConnectionType(url) {
     }
     return 'custom';
 }
-async function run(args) {
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -86,7 +80,7 @@ async function run(args) {
             description: 'Equivalent to --skipCheck --overwrite',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -101,7 +95,7 @@ async function run(args) {
         '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
     ];
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse add-connection <connectionUrlOrPath> [options]',
@@ -113,11 +107,11 @@ async function run(args) {
     if (!connectionUrlOrPath) {
         throw new Error('Missing required argument: connectionUrlOrPath\nUsage: jbrowse add-connection <connectionUrlOrPath> [options]');
     }
-    const target = await (0, utils_ts_1.resolveConfigPath)(flags.target, flags.out);
+    const target = await resolveConfigPath(flags.target, flags.out);
     const { assemblyNames, type, name, config, connectionId, skipCheck, force } = flags;
     const url = await resolveURL(connectionUrlOrPath, !(skipCheck || force));
-    const configContents = await (0, utils_ts_1.readJsonFile)(target);
-    (0, utils_ts_1.debug)(`Using config file ${target}`);
+    const configContents = await readJsonFile(target);
+    debug(`Using config file ${target}`);
     if (!configContents.assemblies?.length) {
         throw new Error('No assemblies found. Please add one before adding connections');
     }
@@ -149,7 +143,7 @@ async function run(args) {
             : type === 'JBrowse1Connection'
                 ? [configContents.assemblies[0]?.name]
                 : undefined,
-        ...(config ? (0, json_parse_better_errors_1.default)(config) : {}),
+        ...(config ? parseJSON(config) : {}),
     };
     if (!configContents.connections) {
         configContents.connections = [];
@@ -166,7 +160,7 @@ async function run(args) {
     else {
         configContents.connections.push(connectionConfig);
     }
-    (0, utils_ts_1.debug)(`Writing configuration to file ${target}`);
-    await (0, utils_ts_1.writeJsonFile)(target, configContents);
+    debug(`Writing configuration to file ${target}`);
+    await writeJsonFile(target, configContents);
     console.log(`${idx !== -1 ? 'Overwrote' : 'Added'} connection "${name || id}" ${idx !== -1 ? 'in' : 'to'} ${target}`);
 }

package/dist/commands/add-track-json.js

@@ -1,10 +1,7 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.run = run;
-const util_1 = require("util");
-const utils_ts_1 = require("../utils.js");
-const config_operations_ts_1 = require("./shared/config-operations.js");
-async function run(args) {
+import { parseArgs } from 'util';
+import { debug, printHelp, readInlineOrFileJson, readJsonFile, resolveConfigPath, } from "../utils.js";
+import { findAndUpdateOrAdd, saveConfigAndReport, } from "./shared/config-operations.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -24,7 +21,7 @@ async function run(args) {
             description: 'Synonym for target',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -35,7 +32,7 @@ async function run(args) {
         '$ jbrowse add-track-json track.json --update',
     ];
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse add-track-json <track> [options]',
@@ -47,16 +44,16 @@ async function run(args) {
     if (!track) {
         throw new Error('Missing required argument: track\nUsage: jbrowse add-track-json <track> [options]');
     }
-    const target = await (0, utils_ts_1.resolveConfigPath)(flags.target, flags.out);
-    (0, utils_ts_1.debug)(`Sequence location is: ${track}`);
+    const target = await resolveConfigPath(flags.target, flags.out);
+    debug(`Sequence location is: ${track}`);
     const { update } = flags;
-    const config = await (0, utils_ts_1.readJsonFile)(target);
-    (0, utils_ts_1.debug)(`Found existing config file ${target}`);
-    const trackConfig = await (0, utils_ts_1.readInlineOrFileJson)(track);
+    const config = await readJsonFile(target);
+    debug(`Found existing config file ${target}`);
+    const trackConfig = await readInlineOrFileJson(track);
     if (!config.tracks) {
         config.tracks = [];
     }
-    const { updatedItems, wasOverwritten } = (0, config_operations_ts_1.findAndUpdateOrAdd)({
+    const { updatedItems, wasOverwritten } = findAndUpdateOrAdd({
         items: config.tracks,
         newItem: trackConfig,
         idField: 'trackId',
@@ -65,7 +62,7 @@ async function run(args) {
         itemType: 'track',
     });
     config.tracks = updatedItems;
-    await (0, config_operations_ts_1.saveConfigAndReport)({
+    await saveConfigAndReport({
         config,
         target,
         itemType: 'track',