@jbrowse/cli 3.6.5 → 4.0.0

package/dist/commands/add-track.js

@@ -6,11 +6,11 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
 const path_1 = __importDefault(require("path"));
 const util_1 = require("util");
-const utils_1 = require("../utils");
-const adapter_utils_1 = require("./add-track-utils/adapter-utils");
-const track_config_1 = require("./add-track-utils/track-config");
-const validators_1 = require("./add-track-utils/validators");
-const track_utils_1 = require("./track-utils");
+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) {
     const options = {
         help: {
@@ -122,7 +122,7 @@ async function run(args) {
         '$ jbrowse add-track /url/relative/path.bam --load inPlace',
     ];
     if (flags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse add-track <track> [options]',
@@ -130,50 +130,48 @@ async function run(args) {
         });
         return;
     }
-    (0, validators_1.validateLoadOption)(flags.load);
+    (0, validators_ts_1.validateLoadOption)(flags.load);
     const track = positionals[0];
-    (0, validators_1.validateTrackArg)(track);
-    const { config, skipCheck, force, overwrite, category, description: trackDescription, load, subDir = '', target, protocol = 'uri', out, indexFile: index, bed1, bed2, } = flags;
-    const output = target || out || '.';
-    const targetConfigPath = (0, track_utils_1.resolveTrackConfigPath)(output);
+    (0, validators_ts_1.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_1.createTargetDirectory)(configDir, subDir);
+    (0, validators_ts_1.createTargetDirectory)(configDir, subDir);
     const location = track;
-    const mapLoc = (p) => (0, track_config_1.mapLocationForFiles)(p, load, subDir);
-    let adapter = (0, adapter_utils_1.guessAdapter)({
+    const mapLoc = (p) => (0, track_config_ts_1.mapLocationForFiles)(p, load, subDir);
+    let adapter = (0, adapter_utils_ts_1.guessAdapter)({
         protocol,
         location: mapLoc(location),
         index: index ? mapLoc(index) : undefined,
         bed1: bed1 ? mapLoc(bed1) : undefined,
         bed2: bed2 ? mapLoc(bed2) : undefined,
     });
-    adapter = (0, track_config_1.addSyntenyAssemblyNames)(adapter, flags.assemblyNames);
-    (0, validators_1.validateLoadAndLocation)(location, load);
-    (0, validators_1.validateAdapterType)(adapter.type);
-    const configContents = await (0, track_utils_1.loadTrackConfig)(targetConfigPath);
-    (0, validators_1.validateAssemblies)(configContents, flags.assemblyNames);
-    const trackParams = (0, track_utils_1.buildTrackParams)({
+    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)({
         flags,
         location,
         adapter,
         configContents,
     });
-    const trackConfig = (0, track_utils_1.createTrackConfiguration)({
+    const trackConfig = (0, track_utils_ts_1.createTrackConfiguration)({
         location,
         trackParams,
         flags: { category, description: trackDescription, config },
         adapter,
         configContents,
-        skipCheck,
     });
-    const { updatedConfig, wasOverwritten } = (0, track_utils_1.addTrackToConfig)({
+    const { updatedConfig, wasOverwritten } = (0, track_utils_ts_1.addTrackToConfig)({
         configContents,
         trackConfig,
         trackId: trackParams.trackId,
         force,
         overwrite,
     });
-    await (0, track_utils_1.processTrackFiles)({
+    await (0, track_utils_ts_1.processTrackFiles)({
         location,
         index,
         bed1,
@@ -183,7 +181,7 @@ async function run(args) {
         subDir,
         force,
     });
-    await (0, track_utils_1.saveTrackConfigAndReport)({
+    await (0, track_utils_ts_1.saveTrackConfigAndReport)({
         config: updatedConfig,
         targetConfigPath,
         name: trackParams.name,

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

@@ -0,0 +1,100 @@
+"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) {
+    const options = {
+        help: {
+            type: 'boolean',
+            short: 'h',
+        },
+        port: {
+            type: 'string',
+            short: 'p',
+            description: 'Specified port to start the server on (default: 9090)',
+        },
+        root: {
+            type: 'string',
+            description: 'Path to the root of the JB2 installation',
+        },
+        bodySizeLimit: {
+            type: 'string',
+            description: 'Size limit of the update message (default: 25mb)',
+        },
+    };
+    const { values: flags } = (0, util_1.parseArgs)({
+        args,
+        options,
+        allowPositionals: true,
+    });
+    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)({
+            description,
+            examples,
+            usage: 'jbrowse admin-server [options]',
+            options,
+        });
+        return;
+    }
+    const { root, bodySizeLimit = '25mb' } = flags;
+    const { outFile, baseDir } = await (0, utils_ts_1.setupConfigFile)({ root });
+    // Parse and validate port
+    const port = (0, utils_ts_1.parsePort)({ portStr: flags.port });
+    // Set up the Express server
+    // const { app, key, keyPath, serverRef } = setupServer({
+    //   baseDir,
+    //   outFile,
+    //   bodySizeLimit,
+    // })
+    const app = (0, express_1.default)();
+    // Configure middleware
+    app.use(express_1.default.static(baseDir));
+    app.use((0, cors_1.default)());
+    app.use(express_1.default.json({ limit: bodySizeLimit }));
+    // Add error handling middleware
+    app.use((err, _req, res, next) => {
+        if (err) {
+            console.error('Server error:', err);
+            res.status(500).setHeader('Content-Type', 'text/plain');
+            res.send('Internal Server Error');
+        }
+        else {
+            next();
+        }
+    });
+    // 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}`);
+    try {
+        fs_1.default.writeFileSync(keyPath, key);
+        (0, utils_ts_2.debug)(`Admin key stored at ${keyPath}`);
+    }
+    catch (error) {
+        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
+        // 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)({
+        app,
+        baseDir,
+        outFile,
+        key,
+        serverRef,
+    });
+    // Start the server and set up shutdown handlers
+    (0, utils_ts_1.startServer)({ app, port, key, outFile, keyPath, serverRef });
+}

package/dist/commands/{admin-server-utils.js → admin-server/utils.js}

@@ -8,15 +8,12 @@ exports.parsePort = parsePort;
 exports.generateKey = generateKey;
 exports.setupConfigFile = setupConfigFile;
 exports.setupRoutes = setupRoutes;
-exports.setupServer = setupServer;
 exports.startServer = startServer;
 const crypto_1 = __importDefault(require("crypto"));
 const fs_1 = __importDefault(require("fs"));
-const os_1 = __importDefault(require("os"));
 const path_1 = __importDefault(require("path"));
-const cors_1 = __importDefault(require("cors"));
-const express_1 = __importDefault(require("express"));
-const utils_1 = require("../utils");
+const utils_ts_1 = require("../../utils.js");
+const utils_ts_2 = require("../add-assembly/utils.js");
 /**
  * Validates if a port number is in the valid range
  */
@@ -46,24 +43,14 @@ function generateKey() {
  * Sets up the configuration file
  */
 async function setupConfigFile({ root = '.', } = {}) {
-    const output = root;
-    const isDir = fs_1.default.lstatSync(output).isDirectory();
-    const outFile = isDir ? `${output}/config.json` : output;
+    const outFile = await (0, utils_ts_1.resolveConfigPath)(root);
     const baseDir = path_1.default.dirname(outFile);
     if (fs_1.default.existsSync(outFile)) {
-        (0, utils_1.debug)(`Found existing config file ${outFile}`);
+        (0, utils_ts_1.debug)(`Found existing config file ${outFile}`);
     }
     else {
-        (0, utils_1.debug)(`Creating config file ${outFile}`);
-        await (0, utils_1.writeJsonFile)(outFile, {
-            assemblies: [],
-            configuration: {},
-            connections: [],
-            defaultSession: {
-                name: 'New Session',
-            },
-            tracks: [],
-        });
+        (0, utils_ts_1.debug)(`Creating config file ${outFile}`);
+        await (0, utils_ts_1.writeJsonFile)(outFile, (0, utils_ts_2.createDefaultConfig)());
     }
     return { outFile, baseDir };
 }
@@ -176,44 +163,6 @@ function setupRoutes({ app, baseDir, outFile, key, serverRef, }) {
         });
     });
 }
-/**
- * Sets up the Express server with routes
- */
-function setupServer({ baseDir, outFile, bodySizeLimit, }) {
-    // Create Express application
-    const app = (0, express_1.default)();
-    // Configure middleware
-    app.use(express_1.default.static(baseDir));
-    app.use((0, cors_1.default)());
-    app.use(express_1.default.json({ limit: bodySizeLimit }));
-    // Add error handling middleware
-    app.use((err, _req, res, next) => {
-        if (err) {
-            console.error('Server error:', err);
-            res.status(500).setHeader('Content-Type', 'text/plain');
-            res.send('Internal Server Error');
-        }
-        else {
-            next();
-        }
-    });
-    // Generate admin key and store it
-    const key = generateKey();
-    const keyPath = path_1.default.join(os_1.default.tmpdir(), `jbrowse-admin-${key}`);
-    try {
-        fs_1.default.writeFileSync(keyPath, key);
-        (0, utils_1.debug)(`Admin key stored at ${keyPath}`);
-    }
-    catch (error) {
-        console.error(`Failed to write admin key to ${keyPath}:`, error.message);
-        // Continue anyway, as this is not critical
-    }
-    // Create server reference for shutdown route
-    const serverRef = { current: null };
-    // Set up routes
-    setupRoutes({ app, baseDir, outFile, key, serverRef });
-    return { app, key, keyPath, serverRef };
-}
 /**
  * Starts the server and sets up shutdown handlers
  */
@@ -246,7 +195,7 @@ function startServer({ app, port, key, outFile, keyPath, serverRef, }) {
             // Clean up admin key file
             try {
                 fs_1.default.unlinkSync(keyPath);
-                (0, utils_1.debug)(`Removed admin key file: ${keyPath}`);
+                (0, utils_ts_1.debug)(`Removed admin key file: ${keyPath}`);
             }
             catch (error) {
                 // Ignore errors when cleaning up

package/dist/commands/create.js

@@ -7,8 +7,8 @@ exports.run = run;
 const fs_1 = __importDefault(require("fs"));
 const util_1 = require("util");
 const decompress_1 = __importDefault(require("decompress"));
-const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
-const utils_1 = require("../utils");
+const fetchWithProxy_ts_1 = __importDefault(require("../fetchWithProxy.js"));
+const utils_ts_1 = require("../utils.js");
 const fsPromises = fs_1.default.promises;
 const description = 'Downloads and installs the latest JBrowse 2 release';
 const examples = [
@@ -69,7 +69,7 @@ async function run(args) {
         args,
     });
     if (runFlags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse create [localPath] [options]',
@@ -86,7 +86,7 @@ async function run(args) {
     }
     const { force, url, listVersions, tag, branch, nightly } = runFlags;
     if (listVersions) {
-        const versions = (await (0, utils_1.fetchGithubVersions)()).map(version => version.tag_name);
+        const versions = (await (0, utils_ts_1.fetchGithubVersions)()).map(version => version.tag_name);
         console.log(`All JBrowse versions:\n${versions.join('\n')}`);
         process.exit(0);
     }
@@ -96,11 +96,11 @@ async function run(args) {
         await checkPath(argsPath);
     }
     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)());
+        (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)());
     console.log(`Fetching ${locationUrl}...`);
-    const response = await (0, fetchWithProxy_1.default)(locationUrl);
+    const response = await (0, fetchWithProxy_ts_1.default)(locationUrl);
     if (!response.ok) {
         throw new Error(`HTTP ${response.status} fetching ${locationUrl}: ${response.statusText}`);
     }

package/dist/commands/{make-pif.js → make-pif/index.js}

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
 const util_1 = require("util");
-const utils_1 = require("../utils");
-const pif_generator_1 = require("./make-pif-utils/pif-generator");
-const validators_1 = require("./make-pif-utils/validators");
+const pif_generator_ts_1 = require("./pif-generator.js");
+const utils_ts_1 = require("../../utils.js");
+const validators_ts_1 = require("../shared/validators.js");
 async function run(args) {
     const options = {
         help: {
@@ -32,7 +32,7 @@ async function run(args) {
         '$ jbrowse make-pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also',
     ];
     if (flags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse make-pif <file> [options]',
@@ -41,18 +41,12 @@ async function run(args) {
         return;
     }
     const file = positionals[0];
-    (0, validators_1.validateFileArgument)(file);
-    (0, validators_1.validateRequiredCommands)();
+    (0, validators_ts_1.validateFileArgument)(file, 'make-pif', 'paf');
+    (0, validators_ts_1.validateRequiredCommands)(['sh', 'sort', 'grep', 'tabix', 'bgzip']);
     const { out, csi = false } = flags;
-    const outputFile = (0, pif_generator_1.getOutputFilename)(file, out);
-    try {
-        const child = (0, pif_generator_1.spawnSortProcess)(outputFile, csi);
-        await (0, pif_generator_1.createPIF)(file, child.stdin);
-        child.stdin.end();
-        await (0, pif_generator_1.waitForProcessClose)(child);
-    }
-    catch (error) {
-        console.error('Error during PIF creation:', error);
-        process.exit(1);
-    }
+    const outputFile = (0, pif_generator_ts_1.getOutputFilename)(file, out);
+    const child = (0, pif_generator_ts_1.spawnSortProcess)(outputFile, csi);
+    await (0, pif_generator_ts_1.createPIF)(file, child.stdin);
+    child.stdin.end();
+    await (0, pif_generator_ts_1.waitForProcessClose)(child);
 }

package/dist/commands/{make-pif-utils → make-pif}/pif-generator.js

@@ -9,11 +9,11 @@ exports.getOutputFilename = getOutputFilename;
 exports.waitForProcessClose = waitForProcessClose;
 const child_process_1 = require("child_process");
 const path_1 = __importDefault(require("path"));
-const cigar_utils_1 = require("./cigar-utils");
-const file_utils_1 = require("./file-utils");
+const cigar_utils_ts_1 = require("./cigar-utils.js");
+const file_utils_ts_1 = require("./file-utils.js");
 async function createPIF(filename, stream) {
-    const rl1 = filename ? (0, file_utils_1.getReadline)(filename) : (0, file_utils_1.getStdReadline)();
-    const writeWithBackpressure = (0, file_utils_1.createWriteWithBackpressure)(stream);
+    const rl1 = filename ? (0, file_utils_ts_1.getReadline)(filename) : (0, file_utils_ts_1.getStdReadline)();
+    const writeWithBackpressure = (0, file_utils_ts_1.createWriteWithBackpressure)(stream);
     // Process the file line by line with backpressure handling
     try {
         for await (const line of rl1) {
@@ -24,8 +24,8 @@ async function createPIF(filename, stream) {
             const CIGAR = rest[cigarIdx];
             if (CIGAR) {
                 rest[cigarIdx] = `cg:Z:${strand === '-'
-                    ? (0, cigar_utils_1.flipCigar)((0, cigar_utils_1.parseCigar)(CIGAR.slice(5))).join('')
-                    : (0, cigar_utils_1.swapIndelCigar)(CIGAR.slice(5))}`;
+                    ? (0, cigar_utils_ts_1.flipCigar)((0, cigar_utils_ts_1.parseCigar)(CIGAR.slice(5))).join('')
+                    : (0, cigar_utils_ts_1.swapIndelCigar)(CIGAR.slice(5))}`;
             }
             // Write the second line and handle backpressure
             await writeWithBackpressure(`${[`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t')}\n`);

package/dist/commands/{sort-bed-utils/process-utils.js → process-utils.js}

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.waitForProcessClose = waitForProcessClose;
-exports.handleProcessError = handleProcessError;
 async function waitForProcessClose(child) {
     return new Promise((resolve, reject) => {
         child.on('close', code => {
@@ -12,12 +11,3 @@ async function waitForProcessClose(child) {
         });
     });
 }
-function handleProcessError(error) {
-    if (error instanceof Error) {
-        console.error(`Process error: ${error.message}`);
-    }
-    else {
-        console.error('Unknown process error:', error);
-    }
-    process.exit(1);
-}

package/dist/commands/remove-track.js

@@ -1,9 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
-const fs_1 = require("fs");
 const util_1 = require("util");
-const utils_1 = require("../utils");
+const utils_ts_1 = require("../utils.js");
 async function run(args) {
     const options = {
         help: {
@@ -27,7 +26,7 @@ async function run(args) {
     const description = 'Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!';
     const examples = ['$ jbrowse remove-track trackId'];
     if (flags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse remove-track <trackId> [options]',
@@ -37,14 +36,10 @@ async function run(args) {
     }
     const trackId = positionals[0];
     if (!trackId) {
-        console.error('Error: Missing required argument: trackId');
-        console.error('Usage: jbrowse remove-track <trackId> [options]');
-        process.exit(1);
+        throw new Error('Missing required argument: trackId\nUsage: jbrowse remove-track <trackId> [options]');
     }
-    const output = flags.target || flags.out || '.';
-    const isDir = (await fs_1.promises.lstat(output)).isDirectory();
-    const target = isDir ? `${output}/config.json` : output;
-    const config = await (0, utils_1.readJsonFile)(target);
+    const target = await (0, utils_ts_1.resolveConfigPath)(flags.target, flags.out);
+    const config = await (0, utils_ts_1.readJsonFile)(target);
     const originalLength = config.tracks?.length || 0;
     config.tracks = config.tracks?.filter(({ trackId: id }) => id !== trackId);
     const newLength = config.tracks?.length || 0;
@@ -52,7 +47,7 @@ async function run(args) {
         console.log(`No track found with trackId: ${trackId}`);
     }
     else {
-        await (0, utils_1.writeJsonFile)(target, config);
+        await (0, utils_ts_1.writeJsonFile)(target, config);
         console.log(`Removed track with trackId: ${trackId} from ${target}`);
     }
 }

package/dist/commands/set-default-session.js

@@ -4,11 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
-const fs_1 = __importDefault(require("fs"));
+const fs_1 = require("fs");
 const util_1 = require("util");
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-const utils_1 = require("../utils");
-const fsPromises = fs_1.default.promises;
+const utils_ts_1 = require("../utils.js");
 const description = 'Set a default session with views and tracks';
 const examples = [
     '# set default session for the config.json in your current directory',
@@ -51,7 +50,7 @@ const options = {
 async function run(args) {
     const { values: runFlags } = (0, util_1.parseArgs)({ options, args });
     if (runFlags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse add-track <track> [options]',
@@ -60,23 +59,20 @@ async function run(args) {
         return;
     }
     const { session, currentSession, delete: deleteDefaultSession } = runFlags;
-    const output = runFlags.target || runFlags.out || '.';
-    const isDir = (await fsPromises.lstat(output)).isDirectory();
-    const target = isDir ? `${output}/config.json` : output;
-    const configContents = await (0, utils_1.readJsonFile)(target);
+    const target = await (0, utils_ts_1.resolveConfigPath)(runFlags.target, runFlags.out);
+    const configContents = await (0, utils_ts_1.readJsonFile)(target);
     if (deleteDefaultSession) {
         configContents.defaultSession = undefined;
-        await (0, utils_1.writeJsonFile)(target, configContents);
+        await (0, utils_ts_1.writeJsonFile)(target, configContents);
     }
     else if (currentSession) {
         console.log(`The current default session is ${JSON.stringify(configContents.defaultSession)}`);
-        process.exit();
     }
     else if (!session) {
         throw new Error('Please provide a --session file');
     }
     else if (session) {
-        await (0, utils_1.writeJsonFile)(target, {
+        await (0, utils_ts_1.writeJsonFile)(target, {
             ...configContents,
             defaultSession: await readDefaultSessionFile(session),
         });
@@ -85,7 +81,7 @@ async function run(args) {
 async function readDefaultSessionFile(defaultSessionFile) {
     let defaultSessionJson;
     try {
-        defaultSessionJson = await fsPromises.readFile(defaultSessionFile, {
+        defaultSessionJson = await fs_1.promises.readFile(defaultSessionFile, {
             encoding: 'utf8',
         });
     }

package/dist/commands/shared/config-operations.js

@@ -0,0 +1,37 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.findAndUpdateOrAdd = findAndUpdateOrAdd;
+exports.saveConfigAndReport = saveConfigAndReport;
+const utils_ts_1 = require("../../utils.js");
+/**
+ * Generic function to find and update or add an item to a config array
+ * Returns the updated config and whether an item was overwritten
+ */
+function findAndUpdateOrAdd({ items, newItem, idField, getId, allowOverwrite, itemType, }) {
+    const newId = getId(newItem);
+    const idx = items.findIndex(item => getId(item) === newId);
+    if (idx !== -1) {
+        (0, utils_ts_1.debug)(`Found existing ${itemType} ${newId} in configuration`);
+        if (allowOverwrite) {
+            (0, utils_ts_1.debug)(`Overwriting ${itemType} ${newId} in configuration`);
+            const updatedItems = [...items];
+            updatedItems[idx] = newItem;
+            return { updatedItems, wasOverwritten: true };
+        }
+        else {
+            throw new Error(`Cannot add ${itemType} with ${idField} ${newId}, a ${itemType} with that ${idField} already exists`);
+        }
+    }
+    else {
+        return { updatedItems: [...items, newItem], wasOverwritten: false };
+    }
+}
+/**
+ * Saves a config file and reports the result to the user
+ */
+async function saveConfigAndReport({ config, target, itemType, itemName, itemId, wasOverwritten, }) {
+    (0, utils_ts_1.debug)(`Writing configuration to file ${target}`);
+    await (0, utils_ts_1.writeJsonFile)(target, config);
+    const idPart = itemId ? ` and ${itemType}Id "${itemId}"` : '';
+    console.log(`${wasOverwritten ? 'Overwrote' : 'Added'} ${itemType} with name "${itemName}"${idPart} ${wasOverwritten ? 'in' : 'to'} ${target}`);
+}

package/dist/commands/shared/sort-utils.js

@@ -0,0 +1,57 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GFF_CONFIG = exports.BED_CONFIG = void 0;
+exports.spawnSortProcess = spawnSortProcess;
+const child_process_1 = require("child_process");
+const tmp_1 = __importDefault(require("tmp"));
+exports.BED_CONFIG = {
+    description: 'Helper utility to sort BED files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep',
+    examples: [
+        '# sort bed and pipe to bgzip',
+        '$ jbrowse sort-bed input.bed | bgzip > sorted.bed.gz',
+        '$ tabix sorted.bed.gz',
+        '',
+        '# OR pipe data via stdin: cat file.bed | jbrowse sort-bed | bgzip > sorted.bed.gz',
+    ],
+    sortColumn: 2,
+    fileType: 'bed',
+};
+exports.GFF_CONFIG = {
+    description: 'Helper utility to sort GFF files for tabix. Moves all lines starting with # to the top of the file, and sort by refname and start position using unix utilities sort and grep',
+    examples: [
+        '# sort gff and pipe to bgzip',
+        '$ jbrowse sort-gff input.gff | bgzip > sorted.gff.gz',
+        '$ tabix sorted.gff.gz',
+        '',
+        '# sort gff from stdin',
+        '$ cat input.gff | jbrowse sort-gff | bgzip > sorted.gff.gz',
+    ],
+    sortColumn: 4,
+    fileType: 'gff',
+};
+function getMinimalEnvironment() {
+    return {
+        ...process.env,
+        LC_ALL: 'C',
+    };
+}
+function createSortCommandForStdin(sortColumn) {
+    const tmpFile = tmp_1.default.fileSync({ prefix: 'jbrowse-sort' }).name;
+    const sortCmd = `sort -t"\`printf '\\t'\`" -k1,1 -k${sortColumn},${sortColumn}n`;
+    return `cat > ${tmpFile} && (grep "^#" ${tmpFile}; grep -v "^#" ${tmpFile} | ${sortCmd}) && rm -f ${tmpFile}`;
+}
+function createSortCommandForFile(file, sortColumn) {
+    return `(grep "^#" "${file}"; grep -v "^#" "${file}" | sort -t"\`printf '\\t'\`" -k1,1 -k${sortColumn},${sortColumn}n)`;
+}
+function spawnSortProcess(file, sortColumn) {
+    const command = file
+        ? createSortCommandForFile(file, sortColumn)
+        : createSortCommandForStdin(sortColumn);
+    return (0, child_process_1.spawn)('sh', ['-c', command], {
+        env: getMinimalEnvironment(),
+        stdio: 'inherit',
+    });
+}