@jbrowse/cli 3.5.1 → 3.6.1

package/dist/commands/track-utils.js

@@ -0,0 +1,85 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.resolveTrackConfigPath = resolveTrackConfigPath;
+exports.loadTrackConfig = loadTrackConfig;
+exports.processTrackFiles = processTrackFiles;
+exports.addTrackToConfig = addTrackToConfig;
+exports.saveTrackConfigAndReport = saveTrackConfigAndReport;
+exports.buildTrackParams = buildTrackParams;
+exports.createTrackConfiguration = createTrackConfiguration;
+const fs_1 = __importDefault(require("fs"));
+const path_1 = __importDefault(require("path"));
+const utils_1 = require("../utils");
+const adapter_utils_1 = require("./add-track-utils/adapter-utils");
+const file_operations_1 = require("./add-track-utils/file-operations");
+const track_config_1 = require("./add-track-utils/track-config");
+const validators_1 = require("./add-track-utils/validators");
+function resolveTrackConfigPath(output) {
+    const isDir = fs_1.default.lstatSync(output).isDirectory();
+    return isDir ? `${output}/config.json` : output;
+}
+async function loadTrackConfig(targetConfigPath) {
+    return await (0, utils_1.readJsonFile)(targetConfigPath);
+}
+async function processTrackFiles({ location, index, bed1, bed2, load, configDir, subDir, force, }) {
+    if (load) {
+        await Promise.all(Object.values((0, adapter_utils_1.guessFileNames)({ location, index, bed1, bed2 }))
+            .filter(f => !!f)
+            .map(src => (0, file_operations_1.loadFile)({
+            src,
+            destDir: configDir,
+            mode: load,
+            subDir,
+            force,
+        })));
+    }
+}
+function addTrackToConfig({ configContents, trackConfig, trackId, force, overwrite, }) {
+    const idx = (0, validators_1.validateTrackId)(configContents, trackId, force, overwrite);
+    const updatedConfig = { ...configContents };
+    if (idx !== -1) {
+        (0, utils_1.debug)(`Found existing trackId ${trackId} in configuration`);
+        (0, utils_1.debug)(`Overwriting track ${trackId} in configuration`);
+        updatedConfig.tracks[idx] = trackConfig;
+        return { updatedConfig, wasOverwritten: true };
+    }
+    else {
+        updatedConfig.tracks.push(trackConfig);
+        return { updatedConfig, wasOverwritten: false };
+    }
+}
+async function saveTrackConfigAndReport({ config, targetConfigPath, name, trackId, wasOverwritten, }) {
+    (0, utils_1.debug)(`Writing configuration to file ${targetConfigPath}`);
+    await (0, utils_1.writeJsonFile)(targetConfigPath, config);
+    console.log(`${wasOverwritten ? 'Overwrote' : 'Added'} track with name "${name}" and trackId "${trackId}" ${wasOverwritten ? 'in' : 'to'} ${targetConfigPath}`);
+}
+function buildTrackParams({ flags, location, adapter, configContents, }) {
+    const trackType = flags.trackType || (0, adapter_utils_1.guessTrackType)(adapter.type);
+    const trackId = flags.trackId || path_1.default.basename(location, path_1.default.extname(location));
+    const name = flags.name || trackId;
+    const assemblyNames = flags.assemblyNames || configContents.assemblies?.[0]?.name || '';
+    return {
+        trackType,
+        trackId,
+        name,
+        assemblyNames,
+    };
+}
+function createTrackConfiguration({ location, trackParams, flags, adapter, configContents, skipCheck, }) {
+    return (0, track_config_1.buildTrackConfig)({
+        location,
+        trackType: trackParams.trackType,
+        trackId: trackParams.trackId,
+        name: trackParams.name,
+        assemblyNames: trackParams.assemblyNames,
+        category: flags.category,
+        description: flags.description,
+        config: flags.config,
+        adapter,
+        configContents,
+        skipCheck,
+    });
+}

package/dist/commands/upgrade.js

@@ -0,0 +1,122 @@
+"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 path_1 = __importDefault(require("path"));
+const util_1 = require("util");
+const decompress_1 = __importDefault(require("decompress"));
+const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
+const utils_1 = require("../utils");
+const description = 'Upgrades JBrowse 2 to latest version';
+const examples = [
+    '# Upgrades current directory to latest jbrowse release',
+    '$ jbrowse upgrade',
+    '',
+    '# Upgrade jbrowse instance at a specific filesystem path',
+    '$ jbrowse upgrade /path/to/jbrowse2/installation',
+    '',
+    '# Upgrade to a specific tag',
+    '$ jbrowse upgrade /path/to/jbrowse2/installation --tag v1.0.0',
+    '',
+    '# List versions available on github',
+    '$ jbrowse upgrade --listVersions',
+    '',
+    '# Upgrade from a specific URL',
+    '$ jbrowse upgrade --url https://sample.com/jbrowse2.zip',
+    '',
+    '# Get nightly release from main branch',
+    '$ jbrowse upgrade --nightly',
+];
+const options = {
+    help: {
+        type: 'boolean',
+        short: 'h',
+        description: 'Display help for command',
+    },
+    // will need to account for pagination once there is a lot of releases
+    listVersions: {
+        type: 'boolean',
+        short: 'l',
+        description: 'Lists out all versions of JBrowse 2',
+    },
+    tag: {
+        type: 'string',
+        short: 't',
+        description: 'Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest',
+    },
+    branch: {
+        type: 'string',
+        description: 'Download a development build from a named git branch',
+    },
+    nightly: {
+        type: 'boolean',
+        description: 'Download the latest development build from the main branch',
+    },
+    clean: {
+        type: 'boolean',
+        description: 'Removes old js,map,and LICENSE files in the installation',
+    },
+    url: {
+        type: 'string',
+        short: 'u',
+        description: 'A direct URL to a JBrowse 2 release',
+    },
+};
+async function run(args) {
+    const { positionals, values: runFlags } = (0, util_1.parseArgs)({
+        options,
+        args,
+        allowPositionals: true,
+    });
+    const argsPath = positionals[0];
+    const { clean, listVersions, tag, url, branch, nightly } = runFlags;
+    if (runFlags.help) {
+        (0, utils_1.printHelp)({
+            options,
+            examples,
+            usage: 'jbrowse upgrade [localPath] [options]',
+            description,
+        });
+        return;
+    }
+    if (listVersions) {
+        const versions = (await (0, utils_1.fetchGithubVersions)()).map(v => v.tag_name);
+        console.log(`All JBrowse versions:\n${versions.join('\n')}`);
+        process.exit(0);
+    }
+    if (!argsPath) {
+        throw new Error('No directory supplied');
+    }
+    if (!fs_1.default.existsSync(path_1.default.join(argsPath, 'manifest.json'))) {
+        throw new Error(`No manifest.json found in this directory, are you sure it is an
+        existing jbrowse 2 installation?`);
+    }
+    const locationUrl = url ||
+        (nightly ? await (0, utils_1.getBranch)('main') : '') ||
+        (branch ? await (0, utils_1.getBranch)(branch) : '') ||
+        (tag ? await (0, utils_1.getTag)(tag) : await (0, utils_1.getLatest)());
+    console.log(`Fetching ${locationUrl}...`);
+    const response = await (0, fetchWithProxy_1.default)(locationUrl);
+    if (!response.ok) {
+        throw new Error(`HTTP ${response.status} fetching ${locationUrl}: ${response.statusText}`);
+    }
+    const type = response.headers.get('content-type');
+    if (url &&
+        type !== 'application/zip' &&
+        type !== 'application/octet-stream') {
+        throw new Error('The URL provided does not seem to be a JBrowse installation URL');
+    }
+    if (clean) {
+        fs_1.default.rmSync(path_1.default.join(argsPath, 'static'), { recursive: true, force: true });
+        for (const f of fs_1.default
+            .readdirSync(argsPath)
+            .filter(f => f.includes('worker.js'))) {
+            fs_1.default.unlinkSync(path_1.default.join(argsPath, f));
+        }
+    }
+    await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
+    console.log(`Unpacked ${locationUrl} at ${argsPath}`);
+}

package/dist/index.js

@@ -0,0 +1,119 @@
+#!/usr/bin/env node
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.main = main;
+const fs_1 = __importDefault(require("fs"));
+const path_1 = __importDefault(require("path"));
+const util_1 = require("util");
+// Command imports
+const add_assembly_1 = require("./commands/add-assembly");
+const add_connection_1 = require("./commands/add-connection");
+const add_track_1 = require("./commands/add-track");
+const add_track_json_1 = require("./commands/add-track-json");
+const admin_server_1 = require("./commands/admin-server");
+const create_1 = require("./commands/create");
+const make_pif_1 = require("./commands/make-pif");
+const remove_track_1 = require("./commands/remove-track");
+const set_default_session_1 = require("./commands/set-default-session");
+const sort_bed_1 = require("./commands/sort-bed");
+const sort_gff_1 = require("./commands/sort-gff");
+const text_index_1 = require("./commands/text-index");
+const upgrade_1 = require("./commands/upgrade");
+const commands = {
+    create: create_1.run,
+    'add-assembly': add_assembly_1.run,
+    'add-track': add_track_1.run,
+    'text-index': text_index_1.run,
+    'admin-server': admin_server_1.run,
+    upgrade: upgrade_1.run,
+    'make-pif': make_pif_1.run,
+    'sort-gff': sort_gff_1.run,
+    'sort-bed': sort_bed_1.run,
+    'add-connection': add_connection_1.run,
+    'add-track-json': add_track_json_1.run,
+    'remove-track': remove_track_1.run,
+    'set-default-session': set_default_session_1.run,
+};
+async function main(args) {
+    try {
+        const { values: flags, positionals } = (0, util_1.parseArgs)({
+            args,
+            options: {
+                help: {
+                    type: 'boolean',
+                    short: 'h',
+                    default: false,
+                },
+                version: {
+                    type: 'boolean',
+                    short: 'v',
+                    default: false,
+                },
+            },
+            allowPositionals: true,
+            strict: false, // Allow unknown flags to be passed to subcommands
+        });
+        // Check if help or version is requested at the global level
+        if (flags.help && positionals.length === 0) {
+            showGlobalHelp();
+            return;
+        }
+        if (flags.version && positionals.length === 0) {
+            const packageJson = JSON.parse(fs_1.default.readFileSync(path_1.default.join(__dirname, '../package.json'), 'utf8'));
+            console.log(`@jbrowse/cli version ${packageJson.version}`);
+            return;
+        }
+        const commandName = positionals[0];
+        if (!commandName) {
+            console.error('Error: Missing command');
+            showGlobalHelp();
+            process.exit(1);
+        }
+        const command = commands[commandName];
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!command) {
+            console.error(`Error: Unknown command "${commandName}"`);
+            console.error(`Available commands: ${Object.keys(commands).join(', ')}`);
+            process.exit(1);
+        }
+        // Pass the remaining arguments to the command
+        const commandArgs = args.slice(1); // Remove the command name from args
+        await command(commandArgs);
+    }
+    catch (error) {
+        console.error('Error:', error instanceof Error ? error.message : error);
+        process.exit(1);
+    }
+}
+function showGlobalHelp() {
+    console.log(`
+JBrowse CLI
+
+USAGE
+  $ jbrowse <command> [options]
+
+COMMANDS
+  create               Downloads and installs the latest JBrowse 2 release
+  add-assembly         Add an assembly to a JBrowse 2 configuration
+  add-track            Add a track to a JBrowse 2 configuration
+  text-index           Make a text-indexing file for any given track(s)
+  admin-server         Start up a small admin server for JBrowse configuration
+  upgrade              Upgrades JBrowse 2 to latest version
+  make-pif             Creates pairwise indexed PAF (PIF), with bgzip and tabix
+  sort-gff             Helper utility to sort GFF files for tabix
+  sort-bed             Helper utility to sort BED files for tabix
+  add-connection       Add a connection to a JBrowse 2 configuration
+  add-track-json       Add a track configuration directly from a JSON hunk
+  remove-track         Remove a track configuration from a JBrowse 2 configuration
+  set-default-session  Set a default session with views and tracks
+
+OPTIONS
+  -h, --help     Show help
+  -v, --version  Show version
+
+Use "jbrowse <command> --help" for more information about a command.
+`);
+}

package/dist/utils.js

@@ -0,0 +1,154 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.debug = debug;
+exports.readFile = readFile;
+exports.readJsonFile = readJsonFile;
+exports.writeJsonFile = writeJsonFile;
+exports.resolveFileLocation = resolveFileLocation;
+exports.readInlineOrFileJson = readInlineOrFileJson;
+exports.fetchGithubVersions = fetchGithubVersions;
+exports.getLatest = getLatest;
+exports.fetchVersions = fetchVersions;
+exports.getTag = getTag;
+exports.getBranch = getBranch;
+exports.printHelp = printHelp;
+const fs_1 = require("fs");
+const path_1 = __importDefault(require("path"));
+const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
+const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
+function debug(message) {
+    if (process.env.DEBUG) {
+        console.log(`DEBUG: ${message}`);
+    }
+}
+async function readFile(location) {
+    return fs_1.promises.readFile(location, { encoding: 'utf8' });
+}
+async function readJsonFile(location) {
+    const contents = await fs_1.promises.readFile(location, { encoding: 'utf8' });
+    return (0, json_parse_better_errors_1.default)(contents);
+}
+async function writeJsonFile(location, contents) {
+    debug(`Writing JSON file to ${process.cwd()} ${location}`);
+    return fs_1.promises.writeFile(location, JSON.stringify(contents, null, 2));
+}
+async function resolveFileLocation(location, check = true, inPlace = false) {
+    let locationUrl;
+    try {
+        locationUrl = new URL(location);
+    }
+    catch (error) {
+        // ignore
+    }
+    if (locationUrl) {
+        if (check) {
+            // @ts-expect-error
+            const response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
+            if (!response.ok) {
+                throw new Error(`${locationUrl} result ${response.statusText}`);
+            }
+        }
+        return locationUrl.href;
+    }
+    let locationPath;
+    try {
+        locationPath = check ? await fs_1.promises.realpath(location) : location;
+    }
+    catch (e) {
+        // ignore
+    }
+    if (locationPath) {
+        const filePath = path_1.default.relative(process.cwd(), locationPath);
+        if (inPlace && filePath.startsWith('..')) {
+            console.warn(`Location ${filePath} is not in the JBrowse directory. Make sure it is still in your server directory.`);
+        }
+        return inPlace ? location : filePath;
+    }
+    throw new Error(`Could not resolve to a file or a URL: "${location}"`);
+}
+async function readInlineOrFileJson(inlineOrFileName) {
+    let result;
+    // see if it's inline JSON
+    try {
+        result = (0, json_parse_better_errors_1.default)(inlineOrFileName);
+    }
+    catch (error) {
+        debug(`Not valid inline JSON, attempting to parse as filename: '${inlineOrFileName}'`);
+        // not inline JSON, must be location of a JSON file
+        result = await readJsonFile(inlineOrFileName);
+    }
+    return result;
+}
+async function fetchGithubVersions() {
+    let versions = [];
+    for await (const iter of fetchVersions()) {
+        versions = [...versions, ...iter];
+    }
+    return versions;
+}
+async function getLatest() {
+    for await (const versions of fetchVersions()) {
+        // if a release was just uploaded, or an erroneous build was made then it
+        // might have no build asset
+        const nonprereleases = versions
+            .filter(release => !release.prerelease)
+            .filter(release => release.assets?.length);
+        if (nonprereleases.length > 0) {
+            // @ts-expect-error
+            const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+            if (!file) {
+                throw new Error('no jbrowse-web download found');
+            }
+            return file;
+        }
+    }
+    throw new Error('no version tags found');
+}
+async function* fetchVersions() {
+    let page = 1;
+    let result;
+    do {
+        const url = `https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`;
+        const response = await (0, fetchWithProxy_1.default)(url);
+        if (response.ok) {
+            result = (await response.json());
+            yield result.filter(release => release.tag_name.startsWith('v'));
+            page++;
+        }
+        else {
+            throw new Error(`HTTP ${response.status} fetching ${url}`);
+        }
+    } while (result.length);
+}
+async function getTag(tag) {
+    const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
+    if (response.ok) {
+        const result = (await response.json());
+        const file = result.assets?.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+        if (!file) {
+            throw new Error('Could not find version specified. Use --listVersions to see all available versions');
+        }
+        return file;
+    }
+    throw new Error(`Could not find version: ${response.statusText}`);
+}
+async function getBranch(branch) {
+    return `https://s3.amazonaws.com/jbrowse.org/code/jb2/${branch}/jbrowse-web-${branch}.zip`;
+}
+function printHelp({ description, options, examples, usage, }) {
+    console.log(description);
+    console.log(`\nUsage: ${usage || 'jbrowse <command> [options]'}`);
+    console.log('\nOptions:');
+    for (const [name, option] of Object.entries(options)) {
+        const short = 'short' in option && option.short
+            ? `-${option.short}`
+            : '   ';
+        const namePadded = `--${name}`.padEnd(25, ' ');
+        const desc = option.description?.replace(/\n/g, `\n${' '.repeat(29)}`);
+        console.log(`  ${short}, ${namePadded} ${desc}`);
+    }
+    console.log(`\n${examples.join('\n')}`);
+}

package/package.json

@@ -1,11 +1,10 @@
 {
   "name": "@jbrowse/cli",
-  "version": "3.5.1",
+  "version": "3.6.1",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
-    "jbrowse2",
-    "oclif"
+    "jbrowse2"
   ],
   "license": "Apache-2.0",
   "homepage": "https://jbrowse.org",
@@ -16,39 +15,27 @@
     "directory": "products/jbrowse-cli"
   },
   "author": "JBrowse Team",
-  "main": "lib/index.js",
-  "types": "lib/index.d.ts",
+  "main": "dist/index.js",
   "bin": {
-    "jbrowse": "./bin/run"
+    "jbrowse": "./dist/bin.js"
   },
   "files": [
     "/bin",
-    "/lib",
-    "/npm-shrinkwrap.json",
-    "/oclif.manifest.json"
+    "/bundle",
+    "/dist"
   ],
   "engines": {
-    "node": ">=16"
+    "node": ">=18.3.0"
   },
   "scripts": {
     "prebuild": "npm run clean",
-    "build": "tsc --build",
-    "postpack": "rimraf oclif.manifest.json",
-    "clean": "rimraf lib",
-    "prepack": "npm run clean  && npm run build && npm run manifest && npm run docs",
-    "manifest": "oclif manifest",
-    "version": "npm run docs && npm run docs:version:add",
+    "build": "tsc --build && webpack",
+    "clean": "rimraf dist bundle",
+    "prepack": "npm run clean  && npm run docs",
     "predocs": "npm run build",
-    "docs": "npm run docs:create && npm run docs:format",
-    "docs:create": "oclif readme",
-    "docs:format": "prettier --write README.md",
-    "docs:version:add": "git add README.md"
+    "docs": "./generate_readme.sh > README.md"
   },
   "dependencies": {
-    "@oclif/core": "^4.0.19",
-    "@oclif/plugin-help": "^6.0.15",
-    "boxen": "^4.2.0",
-    "chalk": "^4.1.0",
     "cli-progress": "^3.9.0",
     "command-exists": "^1.2.9",
     "cors": "^2.8.5",
@@ -56,22 +43,10 @@
     "express": "^4.17.1",
     "ixixx": "^2.0.1",
     "json-parse-better-errors": "^1.0.2",
-    "node-fetch-native": "^1.6.4",
-    "tslib": "^2.3.1"
-  },
-  "devDependencies": {
-    "typescript": "^5.1.3"
-  },
-  "oclif": {
-    "commands": "./lib/commands",
-    "bin": "jbrowse",
-    "plugins": [
-      "@oclif/plugin-help"
-    ],
-    "repositoryPrefix": "<%- repo %>/blob/v<%- version %>/products/jbrowse-cli/<%- commandPath %>"
+    "node-fetch-native": "^1.6.4"
   },
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
+  "gitHead": "3b7ba0005a28fb0903b7b31f15259c2cfccecfa1"
 }

package/bin/dev

@@ -1,17 +0,0 @@
-#!/usr/bin/env node
-
-const oclif = require('@oclif/core')
-
-const path = require('path')
-const project = path.join(__dirname, '..', 'tsconfig.json')
-
-// In dev mode -> use ts-node and dev plugins
-process.env.NODE_ENV = 'development'
-
-require('ts-node').register({ project })
-
-// In dev mode, always show stack traces
-oclif.settings.debug = true
-
-// Start the CLI
-oclif.run().then(oclif.flush).catch(oclif.Errors.handle)

package/bin/dev.cmd

@@ -1,3 +0,0 @@
-@echo off
-
-node "%~dp0\dev" %*

package/bin/run.cmd

@@ -1,3 +0,0 @@
-@echo off
-
-node "%~dp0\run" %*