@jbrowse/cli 3.7.0 → 4.0.1

package/dist/bin.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const index_1 = require("./index");
-(0, index_1.main)(process.argv.slice(2)).catch((e) => {
+const index_ts_1 = require("./index.js");
+(0, index_ts_1.main)(process.argv.slice(2)).catch((e) => {
     console.error(e);
 });

package/dist/commands/{add-assembly.js → add-assembly/index.js}

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = run;
 const util_1 = require("util");
-const utils_1 = require("../utils");
-const assembly_utils_1 = require("./assembly-utils");
+const utils_ts_1 = require("./utils.js");
+const utils_ts_2 = require("../../utils.js");
 async function run(args) {
     const options = {
         type: {
@@ -114,7 +114,7 @@ async function run(args) {
         '$ jbrowse add-assembly myfile.fa.gz --load copy',
     ];
     if (runFlags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_2.printHelp)({
             description,
             examples,
             usage: 'jbrowse add-assembly <sequence> [options]',
@@ -124,17 +124,17 @@ async function run(args) {
     }
     const argsSequence = positionals[0] || '';
     const output = runFlags.target || runFlags.out || '.';
-    (0, utils_1.debug)(`Sequence location is: ${argsSequence}`);
-    const target = await (0, assembly_utils_1.resolveTargetPath)(output);
-    const baseAssembly = await (0, assembly_utils_1.getAssembly)({ runFlags, argsSequence, target });
-    const assembly = await (0, assembly_utils_1.enhanceAssembly)(baseAssembly, runFlags);
-    const configContents = await (0, assembly_utils_1.loadOrCreateConfig)(target);
-    const { config: updatedConfig, wasOverwritten } = await (0, assembly_utils_1.addAssemblyToConfig)({
+    (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)({
         config: configContents,
         assembly,
         runFlags,
     });
-    await (0, assembly_utils_1.saveConfigAndReport)({
+    await (0, utils_ts_1.saveConfigAndReport)({
         config: updatedConfig,
         target,
         assembly,

package/dist/commands/{assembly-utils.js → add-assembly/utils.js}

@@ -17,7 +17,9 @@ exports.addAssemblyToConfig = addAssemblyToConfig;
 exports.saveConfigAndReport = saveConfigAndReport;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const utils_1 = require("../utils");
+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) {
     try {
@@ -54,60 +56,26 @@ function guessSequenceType(sequence) {
     throw new Error('Could not determine sequence type automatically, add --type to specify it');
 }
 function needLoadData(location) {
-    let locationUrl;
-    try {
-        locationUrl = new URL(location);
-    }
-    catch (error) {
-        // ignore
-    }
-    if (locationUrl) {
-        return false;
-    }
-    return true;
+    return !(0, common_ts_1.isURL)(location);
 }
 async function loadData({ load, filePaths, destination, }) {
-    let locationUrl;
-    try {
-        locationUrl = new URL(filePaths[0]);
-    }
-    catch (error) {
-        // ignore
+    if ((0, common_ts_1.isURL)(filePaths[0])) {
+        return false;
     }
-    if (locationUrl) {
+    if (load === 'inPlace') {
         return false;
     }
-    switch (load) {
-        case 'copy': {
-            await Promise.all(filePaths.map(async (filePath) => {
-                if (!filePath) {
-                    return undefined;
-                }
-                return copyFile(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
-            }));
-            return true;
-        }
-        case 'symlink': {
-            await Promise.all(filePaths.map(async (filePath) => {
-                if (!filePath) {
-                    return undefined;
-                }
-                return symlink(path_1.default.resolve(filePath), path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
-            }));
-            return true;
-        }
-        case 'move': {
-            await Promise.all(filePaths.map(async (filePath) => {
-                if (!filePath) {
-                    return undefined;
-                }
-                return rename(filePath, path_1.default.join(path_1.default.dirname(destination), path_1.default.basename(filePath)));
-            }));
-            return true;
-        }
-        case 'inPlace': {
-            return false;
-        }
+    const destDir = path_1.default.dirname(destination);
+    const validPaths = filePaths.filter(f => !!f);
+    const operations = {
+        copy: copyFile,
+        symlink: (src, dest) => symlink(path_1.default.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)))));
+        return true;
     }
     return false;
 }
@@ -122,25 +90,25 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
     let { name } = runFlags;
     let { type } = runFlags;
     if (type) {
-        (0, utils_1.debug)(`Type is: ${type}`);
+        (0, utils_ts_1.debug)(`Type is: ${type}`);
     }
     else {
         type = guessSequenceType(argsSequence);
-        (0, utils_1.debug)(`No type specified, guessing type: ${type}`);
+        (0, utils_ts_1.debug)(`No type specified, guessing type: ${type}`);
     }
     if (name) {
-        (0, utils_1.debug)(`Name is: ${name}`);
+        (0, utils_ts_1.debug)(`Name is: ${name}`);
     }
     switch (type) {
         case 'indexedFasta': {
             const { skipCheck, force, load, faiLocation } = runFlags;
-            let sequenceLocation = await (0, utils_1.resolveFileLocation)(argsSequence, !(skipCheck || force), load === 'inPlace');
-            (0, utils_1.debug)(`FASTA location resolved to: ${sequenceLocation}`);
-            let indexLocation = await (0, utils_1.resolveFileLocation)(faiLocation || `${argsSequence}.fai`, !(skipCheck || force), load === 'inPlace');
-            (0, utils_1.debug)(`FASTA index location resolved to: ${indexLocation}`);
+            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}`);
             if (!name) {
                 name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta') ? '.fasta' : '.fa');
-                (0, utils_1.debug)(`Guessing name: ${name}`);
+                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
             }
             const loaded = load
                 ? await loadData({
@@ -168,15 +136,15 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'bgzipFasta': {
-            let sequenceLocation = await (0, utils_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`compressed FASTA location resolved to: ${sequenceLocation}`);
-            let indexLocation = await (0, utils_1.resolveFileLocation)(runFlags.faiLocation || `${sequenceLocation}.fai`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`compressed FASTA index location resolved to: ${indexLocation}`);
-            let bgzipIndexLocation = await (0, utils_1.resolveFileLocation)(runFlags.gziLocation || `${sequenceLocation}.gzi`, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`bgzip index location resolved to: ${bgzipIndexLocation}`);
+            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}`);
             if (!name) {
                 name = path_1.default.basename(sequenceLocation, sequenceLocation.endsWith('.fasta.gz') ? '.fasta.gz' : '.fa.gz');
-                (0, utils_1.debug)(`Guessing name: ${name}`);
+                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -209,11 +177,11 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'twoBit': {
-            let sequenceLocation = await (0, utils_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`2bit location resolved to: ${sequenceLocation}`);
+            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}`);
             if (!name) {
                 name = path_1.default.basename(sequenceLocation, '.2bit');
-                (0, utils_1.debug)(`Guessing name: ${name}`);
+                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -239,11 +207,11 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'chromSizes': {
-            let sequenceLocation = await (0, utils_1.resolveFileLocation)(argsSequence, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`chrom.sizes location resolved to: ${sequenceLocation}`);
+            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}`);
             if (!name) {
                 name = path_1.default.basename(sequenceLocation, '.chrom.sizes');
-                (0, utils_1.debug)(`Guessing name: ${name}`);
+                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
             }
             const loaded = runFlags.load
                 ? await loadData({
@@ -269,8 +237,8 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
             break;
         }
         case 'custom': {
-            const adapter = await (0, utils_1.readInlineOrFileJson)(argsSequence);
-            (0, utils_1.debug)(`Custom adapter: ${JSON.stringify(adapter)}`);
+            const adapter = await (0, utils_ts_1.readInlineOrFileJson)(argsSequence);
+            (0, utils_ts_1.debug)(`Custom adapter: ${JSON.stringify(adapter)}`);
             if (!name) {
                 if (isValidJSON(argsSequence)) {
                     throw new Error('Must provide --name when using custom inline JSON sequence');
@@ -278,7 +246,7 @@ async function getAssembly({ runFlags, argsSequence, target, }) {
                 else {
                     name = path_1.default.basename(argsSequence, '.json');
                 }
-                (0, utils_1.debug)(`Guessing name: ${name}`);
+                (0, utils_ts_1.debug)(`Guessing name: ${name}`);
             }
             if (!('type' in adapter)) {
                 throw new Error(`No "type" specified in sequence adapter "${JSON.stringify(adapter)}"`);
@@ -317,7 +285,7 @@ async function resolveTargetPath(output) {
 async function enhanceAssembly(assembly, runFlags) {
     const enhancedAssembly = { ...assembly };
     if (runFlags.alias?.length) {
-        (0, utils_1.debug)(`Adding assembly aliases: ${runFlags.alias}`);
+        (0, utils_ts_1.debug)(`Adding assembly aliases: ${runFlags.alias}`);
         enhancedAssembly.aliases = runFlags.alias;
     }
     if (runFlags.refNameColors) {
@@ -328,18 +296,18 @@ async function enhanceAssembly(assembly, runFlags) {
     if (runFlags.refNameAliases) {
         if (runFlags.refNameAliasesType &&
             runFlags.refNameAliasesType === 'custom') {
-            const refNameAliasesConfig = await (0, utils_1.readInlineOrFileJson)(runFlags.refNameAliases);
+            const refNameAliasesConfig = await (0, utils_ts_1.readInlineOrFileJson)(runFlags.refNameAliases);
             if (!refNameAliasesConfig.type) {
                 throw new Error(`No "type" specified in refNameAliases adapter "${JSON.stringify(refNameAliasesConfig)}"`);
             }
-            (0, utils_1.debug)(`Adding custom refNameAliases config: ${JSON.stringify(refNameAliasesConfig)}`);
+            (0, utils_ts_1.debug)(`Adding custom refNameAliases config: ${JSON.stringify(refNameAliasesConfig)}`);
             enhancedAssembly.refNameAliases = {
                 adapter: refNameAliasesConfig,
             };
         }
         else {
-            const refNameAliasesLocation = await (0, utils_1.resolveFileLocation)(runFlags.refNameAliases, !(runFlags.skipCheck || runFlags.force), runFlags.load === 'inPlace');
-            (0, utils_1.debug)(`refName aliases file location resolved to: ${refNameAliasesLocation}`);
+            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}`);
             enhancedAssembly.refNameAliases = {
                 adapter: {
                     type: 'RefNameAliasAdapter',
@@ -370,41 +338,37 @@ function createDefaultConfig() {
 async function loadOrCreateConfig(target) {
     const defaultConfig = createDefaultConfig();
     if (fs_1.default.existsSync(target)) {
-        (0, utils_1.debug)(`Found existing config file ${target}`);
+        (0, utils_ts_1.debug)(`Found existing config file ${target}`);
         return {
             ...defaultConfig,
-            ...(await (0, utils_1.readJsonFile)(target)),
+            ...(await (0, utils_ts_1.readJsonFile)(target)),
         };
     }
     else {
-        (0, utils_1.debug)(`Creating config file ${target}`);
+        (0, utils_ts_1.debug)(`Creating config file ${target}`);
         return { ...defaultConfig };
     }
 }
 async function addAssemblyToConfig({ config, assembly, runFlags, }) {
-    const updatedConfig = { ...config };
-    if (!updatedConfig.assemblies) {
-        updatedConfig.assemblies = [];
-    }
-    const idx = updatedConfig.assemblies.findIndex(configAssembly => configAssembly.name === assembly.name);
-    if (idx !== -1) {
-        (0, utils_1.debug)(`Found existing assembly ${assembly.name} in configuration`);
-        if (runFlags.overwrite || runFlags.force) {
-            (0, utils_1.debug)(`Overwriting assembly ${assembly.name} in configuration`);
-            updatedConfig.assemblies[idx] = assembly;
-            return { config: updatedConfig, wasOverwritten: true };
-        }
-        else {
-            throw new Error(`Cannot add assembly with name ${assembly.name}, an assembly with that name already exists`);
-        }
-    }
-    else {
-        updatedConfig.assemblies.push(assembly);
-        return { config: updatedConfig, wasOverwritten: false };
-    }
+    const { updatedItems, wasOverwritten } = (0, config_operations_ts_1.findAndUpdateOrAdd)({
+        items: config.assemblies || [],
+        newItem: assembly,
+        idField: 'name',
+        getId: item => item.name,
+        allowOverwrite: runFlags.overwrite || runFlags.force || false,
+        itemType: 'assembly',
+    });
+    return {
+        config: { ...config, assemblies: updatedItems },
+        wasOverwritten,
+    };
 }
 async function saveConfigAndReport({ config, target, assembly, wasOverwritten, }) {
-    (0, utils_1.debug)(`Writing configuration to file ${target}`);
-    await (0, utils_1.writeJsonFile)(target, config);
-    console.log(`${wasOverwritten ? 'Overwrote' : 'Added'} assembly "${assembly.name}" ${wasOverwritten ? 'in' : 'to'} ${target}`);
+    await (0, config_operations_ts_1.saveConfigAndReport)({
+        config,
+        target,
+        itemType: 'assembly',
+        itemName: assembly.name,
+        wasOverwritten,
+    });
 }

package/dist/commands/add-connection.js

@@ -4,12 +4,11 @@ var __importDefault = (this && this.__importDefault) || function (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 json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
-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");
 async function resolveURL(location, check = true) {
     let locationUrl;
     try {
@@ -19,7 +18,7 @@ async function resolveURL(location, check = true) {
         throw new Error(`The location ${location} provided is not a valid URL`);
     }
     if (check) {
-        const response = await (0, fetchWithProxy_1.default)(`${locationUrl}`, { method: 'HEAD' });
+        const response = await (0, fetchWithProxy_ts_1.default)(`${locationUrl}`, { method: 'HEAD' });
         if (!response.ok) {
             throw new Error(`HTTP ${response.status} fetching ${locationUrl}`);
         }
@@ -102,7 +101,7 @@ async function run(args) {
         '$ 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_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse add-connection <connectionUrlOrPath> [options]',
@@ -112,17 +111,13 @@ async function run(args) {
     }
     const connectionUrlOrPath = positionals[0];
     if (!connectionUrlOrPath) {
-        console.error('Error: Missing required argument: connectionUrlOrPath');
-        console.error('Usage: jbrowse add-connection <connectionUrlOrPath> [options]');
-        process.exit(1);
+        throw new Error('Missing required argument: connectionUrlOrPath\nUsage: jbrowse add-connection <connectionUrlOrPath> [options]');
     }
-    const output = flags.target || flags.out || '.';
-    const isDir = fs_1.default.lstatSync(output).isDirectory();
-    const target = isDir ? `${output}/config.json` : output;
+    const target = await (0, utils_ts_1.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_1.readJsonFile)(target);
-    (0, utils_1.debug)(`Using config file ${target}`);
+    const configContents = await (0, utils_ts_1.readJsonFile)(target);
+    (0, utils_ts_1.debug)(`Using config file ${target}`);
     if (!configContents.assemblies?.length) {
         throw new Error('No assemblies found. Please add one before adding connections');
     }
@@ -171,7 +166,7 @@ async function run(args) {
     else {
         configContents.connections.push(connectionConfig);
     }
-    (0, utils_1.debug)(`Writing configuration to file ${target}`);
-    await (0, utils_1.writeJsonFile)(target, configContents);
+    (0, utils_ts_1.debug)(`Writing configuration to file ${target}`);
+    await (0, utils_ts_1.writeJsonFile)(target, configContents);
     console.log(`${idx !== -1 ? 'Overwrote' : 'Added'} connection "${name || id}" ${idx !== -1 ? 'in' : 'to'} ${target}`);
 }

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

@@ -1,9 +1,9 @@
 "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");
+const config_operations_ts_1 = require("./shared/config-operations.js");
 async function run(args) {
     const options = {
         help: {
@@ -35,7 +35,7 @@ async function run(args) {
         '$ jbrowse add-track-json track.json --update',
     ];
     if (flags.help) {
-        (0, utils_1.printHelp)({
+        (0, utils_ts_1.printHelp)({
             description,
             examples,
             usage: 'jbrowse add-track-json <track> [options]',
@@ -45,37 +45,32 @@ async function run(args) {
     }
     const track = positionals[0];
     if (!track) {
-        console.error('Error: Missing required argument: track');
-        console.error('Usage: jbrowse add-track-json <track> [options]');
-        process.exit(1);
+        throw new Error('Missing required argument: track\nUsage: jbrowse add-track-json <track> [options]');
     }
-    const output = flags.target || flags.out || '.';
-    const isDir = (await fs_1.promises.lstat(output)).isDirectory();
-    const target = isDir ? `${output}/config.json` : output;
-    (0, utils_1.debug)(`Sequence location is: ${track}`);
+    const target = await (0, utils_ts_1.resolveConfigPath)(flags.target, flags.out);
+    (0, utils_ts_1.debug)(`Sequence location is: ${track}`);
     const { update } = flags;
-    const config = await (0, utils_1.readJsonFile)(target);
-    (0, utils_1.debug)(`Found existing config file ${target}`);
-    const trackConfig = await (0, utils_1.readInlineOrFileJson)(track);
+    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);
     if (!config.tracks) {
         config.tracks = [];
     }
-    const idx = config.tracks.findIndex(({ trackId }) => trackId === trackConfig.trackId);
-    if (idx !== -1) {
-        const existing = config.tracks[idx]?.name;
-        (0, utils_1.debug)(`Found existing track ${existing} in configuration`);
-        if (update) {
-            (0, utils_1.debug)(`Overwriting track ${existing} in configuration`);
-            config.tracks[idx] = trackConfig;
-        }
-        else {
-            throw new Error(`Cannot add track ${trackConfig.name}, a track with that trackId already exists: ${existing}`);
-        }
-    }
-    else {
-        config.tracks.push(trackConfig);
-    }
-    (0, utils_1.debug)(`Writing configuration to file ${target}`);
-    await (0, utils_1.writeJsonFile)(target, config);
-    console.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track "${trackConfig.name}" ${idx !== -1 ? 'in' : 'to'} ${target}`);
+    const { updatedItems, wasOverwritten } = (0, config_operations_ts_1.findAndUpdateOrAdd)({
+        items: config.tracks,
+        newItem: trackConfig,
+        idField: 'trackId',
+        getId: item => item.trackId,
+        allowOverwrite: update ?? false,
+        itemType: 'track',
+    });
+    config.tracks = updatedItems;
+    await (0, config_operations_ts_1.saveConfigAndReport)({
+        config,
+        target,
+        itemType: 'track',
+        itemName: trackConfig.name,
+        itemId: trackConfig.trackId,
+        wasOverwritten,
+    });
 }

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

@@ -8,7 +8,7 @@ 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 validators_1 = require("./validators");
+const common_ts_1 = require("../../types/common.js");
 const SYNTENY_ADAPTERS = new Set([
     'PAFAdapter',
     'PairwiseIndexedPAFAdapter',
@@ -19,11 +19,11 @@ const SYNTENY_ADAPTERS = new Set([
     'MCScanSimpleAnchorsAdapter',
 ]);
 function mapLocationForFiles(p, load, subDir) {
-    return !p || (0, validators_1.isUrl)(p) || load === 'inPlace'
+    return !p || (0, common_ts_1.isURL)(p) || load === 'inPlace'
         ? p
         : path_1.default.join(subDir || '', path_1.default.basename(p));
 }
-function buildTrackConfig({ location, trackType, trackId, name, assemblyNames, category, description, config, adapter, configContents, skipCheck, }) {
+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));
     const finalName = name || finalTrackId;
@@ -38,18 +38,6 @@ function buildTrackConfig({ location, trackType, trackId, name, assemblyNames, c
         description,
         ...configObj,
     };
-    // Special handling for AlignmentsTrack
-    if (trackType === 'AlignmentsTrack') {
-        const assembly = configContents.assemblies?.find(asm => asm.name === finalAssemblyNames);
-        if (assembly) {
-            // @ts-expect-error
-            trackConfig.adapter.sequenceAdapter = assembly.sequence.adapter;
-        }
-        else if (!skipCheck) {
-            console.error(`Error: Failed to find assemblyName ${finalAssemblyNames}`);
-            process.exit(1);
-        }
-    }
     return trackConfig;
 }
 function addSyntenyAssemblyNames(adapter, assemblyNames) {

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

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.isUrl = void 0;
 exports.validateLoadOption = validateLoadOption;
 exports.validateTrackArg = validateTrackArg;
 exports.validateLoadAndLocation = validateLoadAndLocation;
@@ -13,8 +12,7 @@ exports.validateTrackId = validateTrackId;
 exports.createTargetDirectory = createTargetDirectory;
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
-const isUrl = (loc) => loc?.match(/^https?:\/\//);
-exports.isUrl = isUrl;
+const common_ts_1 = require("../../types/common.js");
 function validateLoadOption(load) {
     if (load && !['copy', 'symlink', 'move', 'inPlace'].includes(load)) {
         throw new Error('Error: --load must be one of: copy, symlink, move, inPlace');
@@ -22,17 +20,14 @@ function validateLoadOption(load) {
 }
 function validateTrackArg(track) {
     if (!track) {
-        console.error('Missing 1 required arg:');
-        console.error('track  Track file or URL');
-        console.error('See more help with --help');
-        process.exit(1);
+        throw new Error('Missing 1 required arg:\ntrack  Track file or URL\nSee more help with --help');
     }
 }
 function validateLoadAndLocation(location, load) {
-    if (isUrl(location) && load) {
+    if ((0, common_ts_1.isURL)(location) && load) {
         throw new Error('The --load flag is used for local files only, but a URL was provided');
     }
-    else if (!isUrl(location) && !load) {
+    else if (!(0, common_ts_1.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)`);