@jbrowse/cli 4.0.4 → 4.1.3

package/dist/commands/add-track-utils/adapter-utils.js

@@ -1,11 +1,4 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.adapterTypesToTrackTypeMap = void 0;
-exports.makeLocationProtocol = makeLocationProtocol;
-exports.guessFileNames = guessFileNames;
-exports.guessAdapter = guessAdapter;
-exports.guessTrackType = guessTrackType;
-function makeLocationProtocol(protocol) {
+export function makeLocationProtocol(protocol) {
     return (location) => {
         if (protocol === 'uri') {
             return {
@@ -22,7 +15,7 @@ function makeLocationProtocol(protocol) {
         throw new Error(`invalid protocol ${protocol}`);
     };
 }
-function guessFileNames({ location, index, bed1, bed2, }) {
+export function guessFileNames({ location, index, bed1, bed2, }) {
     if (/\.anchors(.simple)?$/i.test(location)) {
         return {
             file: location,
@@ -85,7 +78,7 @@ function guessFileNames({ location, index, bed1, bed2, }) {
     }
     return {};
 }
-function guessAdapter({ location, protocol, index, bed1, bed2, }) {
+export function guessAdapter({ location, protocol, index, bed1, bed2, }) {
     const makeLocation = makeLocationProtocol(protocol);
     if (/\.bam$/i.test(location)) {
         return {
@@ -279,7 +272,7 @@ function guessAdapter({ location, protocol, index, bed1, bed2, }) {
         type: 'UNKNOWN',
     };
 }
-exports.adapterTypesToTrackTypeMap = {
+export const adapterTypesToTrackTypeMap = {
     BamAdapter: 'AlignmentsTrack',
     CramAdapter: 'AlignmentsTrack',
     BgzipFastaAdapter: 'ReferenceSequenceTrack',
@@ -299,6 +292,6 @@ exports.adapterTypesToTrackTypeMap = {
     MCScanAnchorsAdapter: 'SyntenyTrack',
     MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
 };
-function guessTrackType(adapterType) {
-    return exports.adapterTypesToTrackTypeMap[adapterType] || 'FeatureTrack';
+export function guessTrackType(adapterType) {
+    return adapterTypesToTrackTypeMap[adapterType] || 'FeatureTrack';
 }

package/dist/commands/add-track-utils/file-operations.js

@@ -1,24 +1,18 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.loadFile = loadFile;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const { copyFile, rename, symlink, unlink } = fs_1.default.promises;
-const { COPYFILE_EXCL } = fs_1.default.constants;
-async function loadFile({ src, destDir, mode, subDir = '', force = false, }) {
+import fs from 'fs';
+import path from 'path';
+const { copyFile, rename, symlink, unlink } = fs.promises;
+const { COPYFILE_EXCL } = fs.constants;
+export async function loadFile({ src, destDir, mode, subDir = '', force = false, }) {
     if (mode === 'inPlace') {
         return;
     }
-    const dest = path_1.default.join(destDir, subDir, path_1.default.basename(src));
+    const dest = path.join(destDir, subDir, path.basename(src));
     if (force) {
         try {
             await unlink(dest);
         }
         catch (e) {
-            if (e.code !== 'ENOENT') {
+            if (e && typeof e === 'object' && 'code' in e && e.code !== 'ENOENT') {
                 throw e;
             }
         }
@@ -30,7 +24,7 @@ async function loadFile({ src, destDir, mode, subDir = '', force = false, }) {
         return rename(src, dest);
     }
     if (mode === 'symlink') {
-        return symlink(path_1.default.resolve(src), dest);
+        return symlink(path.resolve(src), dest);
     }
     return undefined;
 }

package/dist/commands/add-track-utils/track-config.js

@@ -1,14 +1,6 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.mapLocationForFiles = mapLocationForFiles;
-exports.buildTrackConfig = buildTrackConfig;
-exports.addSyntenyAssemblyNames = addSyntenyAssemblyNames;
-const path_1 = __importDefault(require("path"));
-const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const common_ts_1 = require("../../types/common.js");
+import path from 'path';
+import parseJSON from 'json-parse-better-errors';
+import { isURL } from "../../types/common.js";
 const SYNTENY_ADAPTERS = new Set([
     'PAFAdapter',
     'PairwiseIndexedPAFAdapter',
@@ -18,14 +10,14 @@ const SYNTENY_ADAPTERS = new Set([
     'MCScanAnchorsAdapter',
     'MCScanSimpleAnchorsAdapter',
 ]);
-function mapLocationForFiles(p, load, subDir) {
-    return !p || (0, common_ts_1.isURL)(p) || load === 'inPlace'
+export function mapLocationForFiles(p, load, subDir) {
+    return !p || isURL(p) || load === 'inPlace'
         ? p
-        : path_1.default.join(subDir || '', path_1.default.basename(p));
+        : path.join(subDir || '', path.basename(p));
 }
-function buildTrackConfig({ location, trackType, trackId, name, assemblyNames, category, description, config, adapter, configContents, }) {
-    const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
-    const finalTrackId = trackId || path_1.default.basename(location, path_1.default.extname(location));
+export function buildTrackConfig({ location, trackType, trackId, name, assemblyNames, category, description, config, adapter, configContents, }) {
+    const configObj = config ? parseJSON(config) : {};
+    const finalTrackId = trackId || path.basename(location, path.extname(location));
     const finalName = name || finalTrackId;
     const finalAssemblyNames = assemblyNames || configContents.assemblies?.[0]?.name || '';
     const trackConfig = {
@@ -40,7 +32,7 @@ function buildTrackConfig({ location, trackType, trackId, name, assemblyNames, c
     };
     return trackConfig;
 }
-function addSyntenyAssemblyNames(adapter, assemblyNames) {
+export function addSyntenyAssemblyNames(adapter, assemblyNames) {
     if (SYNTENY_ADAPTERS.has(adapter.type)) {
         return {
             ...adapter,

package/dist/commands/add-track-utils/validators.js

@@ -1,39 +1,27 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.validateLoadOption = validateLoadOption;
-exports.validateTrackArg = validateTrackArg;
-exports.validateLoadAndLocation = validateLoadAndLocation;
-exports.validateAdapterType = validateAdapterType;
-exports.validateAssemblies = validateAssemblies;
-exports.validateTrackId = validateTrackId;
-exports.createTargetDirectory = createTargetDirectory;
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const common_ts_1 = require("../../types/common.js");
-function validateLoadOption(load) {
+import fs from 'fs';
+import path from 'path';
+import { isURL } from "../../types/common.js";
+export function validateLoadOption(load) {
     if (load && !['copy', 'symlink', 'move', 'inPlace'].includes(load)) {
         throw new Error('Error: --load must be one of: copy, symlink, move, inPlace');
     }
 }
-function validateTrackArg(track) {
+export function validateTrackArg(track) {
     if (!track) {
         throw new Error('Missing 1 required arg:\ntrack  Track file or URL\nSee more help with --help');
     }
 }
-function validateLoadAndLocation(location, load) {
-    if ((0, common_ts_1.isURL)(location) && load) {
+export function validateLoadAndLocation(location, load) {
+    if (isURL(location) && load) {
         throw new Error('The --load flag is used for local files only, but a URL was provided');
     }
-    else if (!(0, common_ts_1.isURL)(location) && !load) {
+    else if (!isURL(location) && !load) {
         throw new Error(`The --load flag should be used if a local file is used, example --load
         copy to copy the file into the config directory. Options for load are
         copy/move/symlink/inPlace (inPlace for no file operations)`);
     }
 }
-function validateAdapterType(adapterType) {
+export function validateAdapterType(adapterType) {
     if (adapterType === 'UNKNOWN') {
         throw new Error('Track type is not recognized');
     }
@@ -41,7 +29,7 @@ function validateAdapterType(adapterType) {
         throw new Error('Track type is not supported');
     }
 }
-function validateAssemblies(configContents, assemblyNames) {
+export function validateAssemblies(configContents, assemblyNames) {
     if (!configContents.assemblies?.length) {
         throw new Error('No assemblies found. Please add one before adding tracks');
     }
@@ -49,7 +37,7 @@ function validateAssemblies(configContents, assemblyNames) {
         throw new Error('Too many assemblies, cannot default to one. Please specify the assembly with the --assemblyNames flag');
     }
 }
-function validateTrackId(configContents, trackId, force, overwrite) {
+export function validateTrackId(configContents, trackId, force, overwrite) {
     if (!configContents.tracks) {
         configContents.tracks = [];
     }
@@ -59,11 +47,11 @@ function validateTrackId(configContents, trackId, force, overwrite) {
     }
     return idx;
 }
-function createTargetDirectory(configDir, subDir) {
+export function createTargetDirectory(configDir, subDir) {
     if (subDir) {
-        const dir = path_1.default.join(configDir, subDir);
-        if (!fs_1.default.existsSync(dir)) {
-            fs_1.default.mkdirSync(dir);
+        const dir = path.join(configDir, subDir);
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir);
         }
     }
 }

package/dist/commands/add-track.js

@@ -1,17 +1,11 @@
-"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 utils_ts_1 = require("../utils.js");
-const adapter_utils_ts_1 = require("./add-track-utils/adapter-utils.js");
-const track_config_ts_1 = require("./add-track-utils/track-config.js");
-const validators_ts_1 = require("./add-track-utils/validators.js");
-const track_utils_ts_1 = require("./track-utils.js");
-async function run(args) {
+import path from 'path';
+import { parseArgs } from 'util';
+import { printHelp, resolveConfigPath } from "../utils.js";
+import { guessAdapter } from "./add-track-utils/adapter-utils.js";
+import { addSyntenyAssemblyNames, mapLocationForFiles, } from "./add-track-utils/track-config.js";
+import { createTargetDirectory, validateAdapterType, validateAssemblies, validateLoadAndLocation, validateLoadOption, validateTrackArg, } from "./add-track-utils/validators.js";
+import { addTrackToConfig, buildTrackParams, createTrackConfiguration, loadTrackConfig, processTrackFiles, saveTrackConfigAndReport, } from "./track-utils.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -96,7 +90,7 @@ async function run(args) {
             description: 'Used only for mcscan anchors/simpleAnchors types',
         },
     };
-    const { values: flags, positionals } = (0, util_1.parseArgs)({
+    const { values: flags, positionals } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -122,7 +116,7 @@ async function run(args) {
         '$ jbrowse add-track /url/relative/path.bam --load inPlace',
     ];
     if (flags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse add-track <track> [options]',
@@ -130,48 +124,48 @@ async function run(args) {
         });
         return;
     }
-    (0, validators_ts_1.validateLoadOption)(flags.load);
+    validateLoadOption(flags.load);
     const track = positionals[0];
-    (0, validators_ts_1.validateTrackArg)(track);
+    validateTrackArg(track);
     const { config, force, overwrite, category, description: trackDescription, load, subDir = '', target, protocol = 'uri', out, indexFile: index, bed1, bed2, } = flags;
-    const targetConfigPath = await (0, utils_ts_1.resolveConfigPath)(target, out);
-    const configDir = path_1.default.dirname(targetConfigPath);
-    (0, validators_ts_1.createTargetDirectory)(configDir, subDir);
+    const targetConfigPath = await resolveConfigPath(target, out);
+    const configDir = path.dirname(targetConfigPath);
+    createTargetDirectory(configDir, subDir);
     const location = track;
-    const mapLoc = (p) => (0, track_config_ts_1.mapLocationForFiles)(p, load, subDir);
-    let adapter = (0, adapter_utils_ts_1.guessAdapter)({
+    const mapLoc = (p) => mapLocationForFiles(p, load, subDir);
+    let adapter = guessAdapter({
         protocol,
         location: mapLoc(location),
         index: index ? mapLoc(index) : undefined,
         bed1: bed1 ? mapLoc(bed1) : undefined,
         bed2: bed2 ? mapLoc(bed2) : undefined,
     });
-    adapter = (0, track_config_ts_1.addSyntenyAssemblyNames)(adapter, flags.assemblyNames);
-    (0, validators_ts_1.validateLoadAndLocation)(location, load);
-    (0, validators_ts_1.validateAdapterType)(adapter.type);
-    const configContents = await (0, track_utils_ts_1.loadTrackConfig)(targetConfigPath);
-    (0, validators_ts_1.validateAssemblies)(configContents, flags.assemblyNames);
-    const trackParams = (0, track_utils_ts_1.buildTrackParams)({
+    adapter = addSyntenyAssemblyNames(adapter, flags.assemblyNames);
+    validateLoadAndLocation(location, load);
+    validateAdapterType(adapter.type);
+    const configContents = await loadTrackConfig(targetConfigPath);
+    validateAssemblies(configContents, flags.assemblyNames);
+    const trackParams = buildTrackParams({
         flags,
         location,
         adapter,
         configContents,
     });
-    const trackConfig = (0, track_utils_ts_1.createTrackConfiguration)({
+    const trackConfig = createTrackConfiguration({
         location,
         trackParams,
         flags: { category, description: trackDescription, config },
         adapter,
         configContents,
     });
-    const { updatedConfig, wasOverwritten } = (0, track_utils_ts_1.addTrackToConfig)({
+    const { updatedConfig, wasOverwritten } = addTrackToConfig({
         configContents,
         trackConfig,
         trackId: trackParams.trackId,
         force,
         overwrite,
     });
-    await (0, track_utils_ts_1.processTrackFiles)({
+    await processTrackFiles({
         location,
         index,
         bed1,
@@ -181,7 +175,7 @@ async function run(args) {
         subDir,
         force,
     });
-    await (0, track_utils_ts_1.saveTrackConfigAndReport)({
+    await saveTrackConfigAndReport({
         config: updatedConfig,
         targetConfigPath,
         name: trackParams.name,

package/dist/commands/admin-server/index.js

@@ -1,18 +1,12 @@
-"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 fs_1 = __importDefault(require("fs"));
-const os_1 = __importDefault(require("os"));
-const path_1 = __importDefault(require("path"));
-const util_1 = require("util");
-const cors_1 = __importDefault(require("cors"));
-const express_1 = __importDefault(require("express"));
-const utils_ts_1 = require("./utils.js");
-const utils_ts_2 = require("../../utils.js");
-async function run(args) {
+import fs from 'fs';
+import os from 'os';
+import path from 'path';
+import { parseArgs } from 'util';
+import cors from 'cors';
+import express from 'express';
+import { generateKey, parsePort, setupConfigFile, setupRoutes, startServer, } from "./utils.js";
+import { debug, printHelp } from "../../utils.js";
+export async function run(args) {
     const options = {
         help: {
             type: 'boolean',
@@ -32,7 +26,7 @@ async function run(args) {
             description: 'Size limit of the update message (default: 25mb)',
         },
     };
-    const { values: flags } = (0, util_1.parseArgs)({
+    const { values: flags } = parseArgs({
         args,
         options,
         allowPositionals: true,
@@ -40,7 +34,7 @@ async function run(args) {
     const description = 'Start up a small admin server for JBrowse configuration';
     const examples = ['$ jbrowse admin-server', '$ jbrowse admin-server -p 8888'];
     if (flags.help) {
-        (0, utils_ts_2.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse admin-server [options]',
@@ -49,20 +43,20 @@ async function run(args) {
         return;
     }
     const { root, bodySizeLimit = '25mb' } = flags;
-    const { outFile, baseDir } = await (0, utils_ts_1.setupConfigFile)({ root });
+    const { outFile, baseDir } = await setupConfigFile({ root });
     // Parse and validate port
-    const port = (0, utils_ts_1.parsePort)({ portStr: flags.port });
+    const port = parsePort({ portStr: flags.port });
     // Set up the Express server
     // const { app, key, keyPath, serverRef } = setupServer({
     //   baseDir,
     //   outFile,
     //   bodySizeLimit,
     // })
-    const app = (0, express_1.default)();
+    const app = express();
     // Configure middleware
-    app.use(express_1.default.static(baseDir));
-    app.use((0, cors_1.default)());
-    app.use(express_1.default.json({ limit: bodySizeLimit }));
+    app.use(express.static(baseDir));
+    app.use(cors());
+    app.use(express.json({ limit: bodySizeLimit }));
     // Add error handling middleware
     app.use((err, _req, res, next) => {
         if (err) {
@@ -75,20 +69,20 @@ async function run(args) {
         }
     });
     // Generate admin key and store it
-    const key = (0, utils_ts_1.generateKey)();
-    const keyPath = path_1.default.join(os_1.default.tmpdir(), `jbrowse-admin-${key}`);
+    const key = generateKey();
+    const keyPath = path.join(os.tmpdir(), `jbrowse-admin-${key}`);
     try {
-        fs_1.default.writeFileSync(keyPath, key);
-        (0, utils_ts_2.debug)(`Admin key stored at ${keyPath}`);
+        fs.writeFileSync(keyPath, key);
+        debug(`Admin key stored at ${keyPath}`);
     }
     catch (error) {
-        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
+        console.error(`Failed to write admin key to ${keyPath}:`, error instanceof Error ? error.message : error);
         // Continue anyway, as this is not critical
     }
     // Create server reference for shutdown route
     const serverRef = { current: null };
     // Set up routes
-    (0, utils_ts_1.setupRoutes)({
+    setupRoutes({
         app,
         baseDir,
         outFile,
@@ -96,5 +90,5 @@ async function run(args) {
         serverRef,
     });
     // Start the server and set up shutdown handlers
-    (0, utils_ts_1.startServer)({ app, port, key, outFile, keyPath, serverRef });
+    startServer({ app, port, key, outFile, keyPath, serverRef });
 }

package/dist/commands/admin-server/utils.js

@@ -1,29 +1,18 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.isValidPort = isValidPort;
-exports.parsePort = parsePort;
-exports.generateKey = generateKey;
-exports.setupConfigFile = setupConfigFile;
-exports.setupRoutes = setupRoutes;
-exports.startServer = startServer;
-const crypto_1 = __importDefault(require("crypto"));
-const fs_1 = __importDefault(require("fs"));
-const path_1 = __importDefault(require("path"));
-const utils_ts_1 = require("../../utils.js");
-const utils_ts_2 = require("../add-assembly/utils.js");
+import crypto from 'crypto';
+import fs from 'fs';
+import path from 'path';
+import { debug, resolveConfigPath, writeJsonFile } from "../../utils.js";
+import { createDefaultConfig } from "../add-assembly/utils.js";
 /**
  * Validates if a port number is in the valid range
  */
-function isValidPort(port) {
+export function isValidPort(port) {
     return port > 0 && port < 65535;
 }
 /**
  * Parses and validates a port string
  */
-function parsePort({ portStr, defaultPort = 9090, }) {
+export function parsePort({ portStr, defaultPort = 9090, }) {
     if (!portStr) {
         return defaultPort;
     }
@@ -36,21 +25,21 @@ function parsePort({ portStr, defaultPort = 9090, }) {
 /**
  * Generates a random alphanumeric string to serve as admin key
  */
-function generateKey() {
-    return crypto_1.default.randomBytes(5).toString('hex');
+export function generateKey() {
+    return crypto.randomBytes(5).toString('hex');
 }
 /**
  * Sets up the configuration file
  */
-async function setupConfigFile({ root = '.', } = {}) {
-    const outFile = await (0, utils_ts_1.resolveConfigPath)(root);
-    const baseDir = path_1.default.dirname(outFile);
-    if (fs_1.default.existsSync(outFile)) {
-        (0, utils_ts_1.debug)(`Found existing config file ${outFile}`);
+export async function setupConfigFile({ root = '.', } = {}) {
+    const outFile = await resolveConfigPath(root);
+    const baseDir = path.dirname(outFile);
+    if (fs.existsSync(outFile)) {
+        debug(`Found existing config file ${outFile}`);
     }
     else {
-        (0, utils_ts_1.debug)(`Creating config file ${outFile}`);
-        await (0, utils_ts_1.writeJsonFile)(outFile, (0, utils_ts_2.createDefaultConfig)());
+        debug(`Creating config file ${outFile}`);
+        await writeJsonFile(outFile, createDefaultConfig());
     }
     return { outFile, baseDir };
 }
@@ -71,13 +60,13 @@ function validateAndExtractParams({ req, key, baseDir, outFile, }) {
     try {
         // Normalize the config path
         const configPath = configPathParam
-            ? path_1.default.normalize(path_1.default.join(baseDir, configPathParam))
+            ? path.normalize(path.join(baseDir, configPathParam))
             : outFile;
         // Check for directory traversal attempts
-        const normalizedBaseDir = path_1.default.normalize(baseDir);
-        const relPath = path_1.default.relative(normalizedBaseDir, configPath);
+        const normalizedBaseDir = path.normalize(baseDir);
+        const relPath = path.relative(normalizedBaseDir, configPath);
         // Ensure the config path is within the base directory and doesn't contain path traversal
-        if (relPath.startsWith('..') || path_1.default.isAbsolute(relPath)) {
+        if (relPath.startsWith('..') || path.isAbsolute(relPath)) {
             return { isValid: false, error: 'Cannot perform directory traversal' };
         }
         return { isValid: true, configPath };
@@ -89,7 +78,7 @@ function validateAndExtractParams({ req, key, baseDir, outFile, }) {
 /**
  * Sets up the API routes for the server
  */
-function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
+export function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
     // Root route
     app.get('/', (_req, res) => {
         res.setHeader('Content-Type', 'text/plain');
@@ -110,7 +99,7 @@ function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
             delete body.adminKey;
         }
         try {
-            fs_1.default.writeFileSync(validation.configPath, JSON.stringify(config, null, 2));
+            fs.writeFileSync(validation.configPath, JSON.stringify(config, null, 2));
             res.setHeader('Content-Type', 'text/plain');
             res.send('Config updated successfully');
         }
@@ -128,8 +117,8 @@ function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
             return;
         }
         try {
-            if (fs_1.default.existsSync(validation.configPath)) {
-                const config = fs_1.default.readFileSync(validation.configPath, 'utf8');
+            if (fs.existsSync(validation.configPath)) {
+                const config = fs.readFileSync(validation.configPath, 'utf8');
                 res.setHeader('Content-Type', 'text/plain');
                 res.send(config);
             }
@@ -166,7 +155,7 @@ function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
 /**
  * Starts the server and sets up shutdown handlers
  */
-function startServer({ app, port, key, outFile, keyPath, serverRef, }) {
+export function startServer({ app, port, key, outFile, keyPath, serverRef, }) {
     // Start the server
     const server = app.listen(port, () => {
         console.log(`Admin server started on port ${port}\n\n` +
@@ -194,8 +183,8 @@ function startServer({ app, port, key, outFile, keyPath, serverRef, }) {
         server.close(() => {
             // Clean up admin key file
             try {
-                fs_1.default.unlinkSync(keyPath);
-                (0, utils_ts_1.debug)(`Removed admin key file: ${keyPath}`);
+                fs.unlinkSync(keyPath);
+                debug(`Removed admin key file: ${keyPath}`);
             }
             catch (error) {
                 // Ignore errors when cleaning up

package/dist/commands/create.js

@@ -1,15 +1,9 @@
-"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 fs_1 = __importDefault(require("fs"));
-const util_1 = require("util");
-const decompress_1 = __importDefault(require("decompress"));
-const fetchWithProxy_ts_1 = __importDefault(require("../fetchWithProxy.js"));
-const utils_ts_1 = require("../utils.js");
-const fsPromises = fs_1.default.promises;
+import fs from 'fs';
+import { parseArgs } from 'util';
+import decompress from 'decompress';
+import fetch from "../cliFetch.js";
+import { fetchGithubVersions, getBranch, getLatest, getTag, printHelp, } from "../utils.js";
+const fsPromises = fs.promises;
 const description = 'Downloads and installs the latest JBrowse 2 release';
 const examples = [
     '# Download latest release from github, and put in specific path',
@@ -59,17 +53,17 @@ const options = {
     tag: {
         type: 'string',
         short: 't',
-        description: 'Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest',
+        description: 'Version of JBrowse 2 to install. Format is v1.0.0. Defaults to latest',
     },
 };
-async function run(args) {
-    const { positionals, values: runFlags } = (0, util_1.parseArgs)({
+export async function run(args) {
+    const { positionals, values: runFlags } = parseArgs({
         options,
         allowPositionals: true,
         args,
     });
     if (runFlags.help) {
-        (0, utils_ts_1.printHelp)({
+        printHelp({
             description,
             examples,
             usage: 'jbrowse create [localPath] [options]',
@@ -86,7 +80,7 @@ async function run(args) {
     }
     const { force, url, listVersions, tag, branch, nightly } = runFlags;
     if (listVersions) {
-        const versions = (await (0, utils_ts_1.fetchGithubVersions)()).map(version => version.tag_name);
+        const versions = (await fetchGithubVersions()).map(version => version.tag_name);
         console.log(`All JBrowse versions:\n${versions.join('\n')}`);
         process.exit(0);
     }
@@ -96,11 +90,11 @@ async function run(args) {
         await checkPath(argsPath);
     }
     const locationUrl = url ||
-        (nightly ? await (0, utils_ts_1.getBranch)('main') : '') ||
-        (branch ? await (0, utils_ts_1.getBranch)(branch) : '') ||
-        (tag ? await (0, utils_ts_1.getTag)(tag) : await (0, utils_ts_1.getLatest)());
+        (nightly ? await getBranch('main') : '') ||
+        (branch ? await getBranch(branch) : '') ||
+        (tag ? await getTag(tag) : await getLatest());
     console.log(`Fetching ${locationUrl}...`);
-    const response = await (0, fetchWithProxy_ts_1.default)(locationUrl);
+    const response = await fetch(locationUrl);
     if (!response.ok) {
         throw new Error(`HTTP ${response.status} fetching ${locationUrl}: ${response.statusText}`);
     }
@@ -110,7 +104,7 @@ async function run(args) {
         type !== 'application/octet-stream') {
         throw new Error('The URL provided does not seem to be a JBrowse installation URL');
     }
-    await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
+    await decompress(Buffer.from(await response.arrayBuffer()), argsPath);
     console.log(`Unpacked ${locationUrl} at ${argsPath}`);
 }
 async function checkPath(userPath) {