@jbrowse/cli 2.6.2 → 2.7.0

package/lib/commands/add-track.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const command_1 = require("@oclif/command");
+const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
@@ -27,10 +27,10 @@ function makeLocationProtocol(protocol) {
         throw new Error(`invalid protocol ${protocol}`);
     };
 }
-const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
+const isUrl = (loc) => loc?.match(/^https?:\/\//);
 class AddTrack extends base_1.default {
     async run() {
-        const { args: runArgs, flags: runFlags } = this.parse(AddTrack);
+        const { args: runArgs, flags: runFlags } = await this.parse(AddTrack);
         const { track: argsTrack } = runArgs;
         const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, bed1, bed2, } = runFlags;
         const output = target || out || '.';
@@ -87,7 +87,7 @@ class AddTrack extends base_1.default {
         }
         // only add track if there is an existing config.json
         const configContents = await this.readJsonFile(this.target);
-        if (!configContents.assemblies || !configContents.assemblies.length) {
+        if (!configContents.assemblies?.length) {
             this.error('No assemblies found. Please add one before adding tracks', {
                 exit: 150,
             });
@@ -101,9 +101,16 @@ class AddTrack extends base_1.default {
         name = name || trackId;
         assemblyNames = assemblyNames || configContents.assemblies[0].name;
         const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
-        const trackConfig = Object.assign({ type: trackType, trackId,
+        const trackConfig = {
+            type: trackType,
+            trackId,
             name,
-            adapter, category: category === null || category === void 0 ? void 0 : category.split(',').map(c => c.trim()), assemblyNames: assemblyNames.split(',').map(a => a.trim()), description }, configObj);
+            adapter,
+            category: category?.split(',').map(c => c.trim()),
+            assemblyNames: assemblyNames.split(',').map(a => a.trim()),
+            description,
+            ...configObj,
+        };
         // any special track modifications go here
         if (trackType === 'AlignmentsTrack') {
             const assembly = configContents.assemblies.find(asm => asm.name === assemblyNames);
@@ -167,25 +174,23 @@ class AddTrack extends base_1.default {
         if (/\.anchors(.simple)?$/i.test(location)) {
             return {
                 file: location,
-                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
                 bed1: bed1,
-                // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
                 bed2: bed2,
             };
         }
-        if (/\.bam$/i.test(location)) {
+        else if (/\.bam$/i.test(location)) {
             return {
                 file: location,
                 index: index || `${location}.bai`,
             };
         }
-        if (/\.cram$/i.test(location)) {
+        else if (/\.cram$/i.test(location)) {
             return {
                 file: location,
                 index: index || `${location}.crai`,
             };
         }
-        if (/\.gff3?\.b?gz$/i.test(location) ||
+        else if (/\.gff3?\.b?gz$/i.test(location) ||
             /\.vcf\.b?gz$/i.test(location) ||
             /\.bed\.b?gz$/i.test(location)) {
             return {
@@ -193,25 +198,26 @@ class AddTrack extends base_1.default {
                 index: index || `${location}.tbi`,
             };
         }
-        if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
+        else if (/\.(fa|fasta|fas|fna|mfa)$/i.test(location)) {
             return {
                 file: location,
                 index: index || `${location}.fai`,
             };
         }
-        if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
+        else if (/\.(fa|fasta|fas|fna|mfa)\.b?gz$/i.test(location)) {
             return {
                 file: location,
                 index: `${location}.fai`,
                 index2: `${location}.gzi`,
             };
         }
-        if (/\.2bit$/i.test(location) ||
+        else if (/\.2bit$/i.test(location) ||
             /\/trackData.jsonz?$/i.test(location) ||
             /\/sparql$/i.test(location) ||
             /\.out(.gz)?$/i.test(location) ||
             /\.paf(.gz)?$/i.test(location) ||
             /\.delta(.gz)?$/i.test(location) ||
+            /\.bed?$/i.test(location) ||
             /\.(bw|bigwig)$/i.test(location) ||
             /\.(bb|bigbed)$/i.test(location) ||
             /\.vcf$/i.test(location) ||
@@ -233,101 +239,96 @@ class AddTrack extends base_1.default {
                 bamLocation: makeLocation(location),
                 index: {
                     location: makeLocation(index || `${location}.bai`),
-                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'BAI',
+                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'BAI',
                 },
             };
         }
-        if (/\.cram$/i.test(location)) {
+        else if (/\.cram$/i.test(location)) {
             return {
                 type: 'CramAdapter',
                 cramLocation: makeLocation(location),
                 craiLocation: makeLocation(`${location}.crai`),
             };
         }
-        if (/\.gff3?$/i.test(location)) {
+        else if (/\.gff3?$/i.test(location)) {
             return {
                 type: 'Gff3Adapter',
                 gffLocation: makeLocation(location),
             };
         }
-        if (/\.gff3?\.b?gz$/i.test(location)) {
+        else if (/\.gff3?\.b?gz$/i.test(location)) {
             return {
                 type: 'Gff3TabixAdapter',
                 gffGzLocation: makeLocation(location),
                 index: {
                     location: makeLocation(index || `${location}.tbi`),
-                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
+                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.gtf?$/i.test(location)) {
+        else if (/\.gtf?$/i.test(location)) {
             return {
                 type: 'GtfAdapter',
                 gtfLocation: makeLocation(location),
             };
         }
-        if (/\.vcf$/i.test(location)) {
+        else if (/\.vcf$/i.test(location)) {
             return {
                 type: 'VcfAdapter',
                 vcfLocation: makeLocation(location),
             };
         }
-        if (/\.vcf\.b?gz$/i.test(location)) {
+        else if (/\.vcf\.b?gz$/i.test(location)) {
             return {
                 type: 'VcfTabixAdapter',
                 vcfGzLocation: makeLocation(location),
                 index: {
                     location: makeLocation(index || `${location}.tbi`),
-                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
+                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.vcf\.idx$/i.test(location)) {
+        else if (/\.vcf\.idx$/i.test(location)) {
             return {
                 type: 'UNSUPPORTED',
             };
         }
-        if (/\.bed$/i.test(location)) {
+        else if (/\.bed$/i.test(location)) {
             return {
-                type: 'UNSUPPORTED',
+                type: 'BedAdapter',
+                bedLocation: makeLocation(location),
             };
         }
-        if (/\.bed\.b?gz$/i.test(location)) {
+        else if (/\.bed\.b?gz$/i.test(location)) {
             return {
                 type: 'BedTabixAdapter',
                 bedGzLocation: makeLocation(location),
                 index: {
                     location: makeLocation(index || `${location}.tbi`),
-                    indexType: (index === null || index === void 0 ? void 0 : index.toUpperCase().endsWith('CSI')) ? 'CSI' : 'TBI',
+                    indexType: index?.toUpperCase().endsWith('CSI') ? 'CSI' : 'TBI',
                 },
             };
         }
-        if (/\.bed$/i.test(location)) {
-            return {
-                type: 'BedAdapter',
-                bedLocation: makeLocation(location),
-            };
-        }
-        if (/\.(bb|bigbed)$/i.test(location)) {
+        else if (/\.(bb|bigbed)$/i.test(location)) {
             return {
                 type: 'BigBedAdapter',
                 bigBedLocation: makeLocation(location),
             };
         }
-        if (/\.(bw|bigwig)$/i.test(location)) {
+        else if (/\.(bw|bigwig)$/i.test(location)) {
             return {
                 type: 'BigWigAdapter',
                 bigWigLocation: makeLocation(location),
             };
         }
-        if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
+        else if (/\.(fa|fasta|fna|mfa)$/i.test(location)) {
             return {
                 type: 'IndexedFastaAdapter',
                 fastaLocation: makeLocation(location),
                 faiLocation: makeLocation(index || `${location}.fai`),
             };
         }
-        if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
+        else if (/\.(fa|fasta|fna|mfa)\.b?gz$/i.test(location)) {
             return {
                 type: 'BgzipFastaAdapter',
                 fastaLocation: makeLocation(location),
@@ -335,60 +336,60 @@ class AddTrack extends base_1.default {
                 gziLocation: makeLocation(`${location}.gzi`),
             };
         }
-        if (/\.2bit$/i.test(location)) {
+        else if (/\.2bit$/i.test(location)) {
             return {
                 type: 'TwoBitAdapter',
                 twoBitLocation: makeLocation(location),
             };
         }
-        if (/\.sizes$/i.test(location)) {
+        else if (/\.sizes$/i.test(location)) {
             return {
                 type: 'UNSUPPORTED',
             };
         }
-        if (/\/trackData.jsonz?$/i.test(location)) {
+        else if (/\/trackData.jsonz?$/i.test(location)) {
             return {
                 type: 'NCListAdapter',
                 rootUrlTemplate: makeLocation(location),
             };
         }
-        if (/\/sparql$/i.test(location)) {
+        else if (/\/sparql$/i.test(location)) {
             return {
                 type: 'SPARQLAdapter',
                 endpoint: location,
             };
         }
-        if (/\.hic$/i.test(location)) {
+        else if (/\.hic$/i.test(location)) {
             return {
                 type: 'HicAdapter',
                 hicLocation: makeLocation(location),
             };
         }
-        if (/\.paf(.gz)?$/i.test(location)) {
+        else if (/\.paf(.gz)?$/i.test(location)) {
             return {
                 type: 'PAFAdapter',
                 pafLocation: makeLocation(location),
             };
         }
-        if (/\.out(.gz)?$/i.test(location)) {
+        else if (/\.out(.gz)?$/i.test(location)) {
             return {
                 type: 'MashMapAdapter',
                 outLocation: makeLocation(location),
             };
         }
-        if (/\.chain(.gz)?$/i.test(location)) {
+        else if (/\.chain(.gz)?$/i.test(location)) {
             return {
                 type: 'ChainAdapter',
                 chainLocation: makeLocation(location),
             };
         }
-        if (/\.delta(.gz)?$/i.test(location)) {
+        else if (/\.delta(.gz)?$/i.test(location)) {
             return {
                 type: 'DeltaAdapter',
                 deltaLocation: makeLocation(location),
             };
         }
-        if (/\.anchors(.gz)?$/i.test(location)) {
+        else if (/\.anchors(.gz)?$/i.test(location)) {
             return {
                 type: 'MCScanAnchorsAdapter',
                 mcscanAnchorsLocation: makeLocation(location),
@@ -396,7 +397,7 @@ class AddTrack extends base_1.default {
                 bed2Location: bed2 ? makeLocation(bed2) : undefined,
             };
         }
-        if (/\.anchors.simple(.gz)?$/i.test(location)) {
+        else if (/\.anchors.simple(.gz)?$/i.test(location)) {
             return {
                 type: 'MCScanSimpleAnchorsAdapter',
                 mcscanSimpleAnchorsLocation: makeLocation(location),
@@ -418,6 +419,7 @@ class AddTrack extends base_1.default {
             TwoBitAdapter: 'ReferenceSequenceTrack',
             VcfTabixAdapter: 'VariantTrack',
             VcfAdapter: 'VariantTrack',
+            BedAdapter: 'FeatureTrack',
             HicAdapter: 'HicTrack',
             PAFAdapter: 'SyntenyTrack',
             DeltaAdapter: 'SyntenyTrack',
@@ -449,76 +451,75 @@ AddTrack.examples = [
     '# --load inPlace adds a track without doing file operations',
     '$ jbrowse add-track /url/relative/path.bam --load inPlace',
 ];
-AddTrack.args = [
-    {
-        name: 'track',
+AddTrack.args = {
+    track: core_1.Args.string({
         required: true,
         description: `Track file or URL`,
-    },
-];
+    }),
+};
 AddTrack.flags = {
-    trackType: command_1.flags.string({
+    trackType: core_1.Flags.string({
         char: 't',
         description: `Type of track, by default inferred from track file`,
     }),
-    name: command_1.flags.string({
+    name: core_1.Flags.string({
         char: 'n',
         description: 'Name of the track. Will be defaulted to the trackId if none specified',
     }),
-    indexFile: command_1.flags.string({
+    indexFile: core_1.Flags.string({
         description: 'Optional index file for the track',
     }),
-    description: command_1.flags.string({
+    description: core_1.Flags.string({
         char: 'd',
         description: 'Optional description of the track',
     }),
-    assemblyNames: command_1.flags.string({
+    assemblyNames: core_1.Flags.string({
         char: 'a',
         description: 'Assembly name or names for track as comma separated string. If none, will default to the assembly in your config file',
     }),
-    category: command_1.flags.string({
+    category: core_1.Flags.string({
         description: 'Optional Comma separated string of categories to group tracks',
     }),
-    config: command_1.flags.string({
+    config: core_1.Flags.string({
         description: `Any extra config settings to add to a track. i.e '{"defaultRendering": "density"}'`,
     }),
-    target: command_1.flags.string({
+    target: core_1.Flags.string({
         description: 'path to config file in JB2 installation to write out to.',
     }),
-    out: command_1.flags.string({
+    out: core_1.Flags.string({
         description: 'synonym for target',
     }),
-    subDir: command_1.flags.string({
+    subDir: core_1.Flags.string({
         description: 'when using --load a file, output to a subdirectory of the target dir',
         default: '',
     }),
-    help: command_1.flags.help({ char: 'h' }),
-    trackId: command_1.flags.string({
+    help: core_1.Flags.help({ char: 'h' }),
+    trackId: core_1.Flags.string({
         description: 'trackId for the track, by default inferred from filename, must be unique throughout config',
     }),
-    load: command_1.flags.string({
+    load: core_1.Flags.string({
         char: 'l',
         description: 'Required flag when using a local file. Choose how to manage the track. Copy, symlink, or move the track to the JBrowse directory. Or inPlace to leave track alone',
         options: ['copy', 'symlink', 'move', 'inPlace'],
     }),
-    skipCheck: command_1.flags.boolean({
+    skipCheck: core_1.Flags.boolean({
         description: 'Skip check for whether or not the file or URL exists or if you are in a JBrowse directory',
     }),
-    overwrite: command_1.flags.boolean({
+    overwrite: core_1.Flags.boolean({
         description: 'Overwrites existing track if it shares the same trackId',
     }),
-    force: command_1.flags.boolean({
+    force: core_1.Flags.boolean({
         char: 'f',
         description: 'Equivalent to `--skipCheck --overwrite`',
     }),
-    protocol: command_1.flags.string({
+    protocol: core_1.Flags.string({
         description: 'Force protocol to a specific value',
         default: 'uri',
     }),
-    bed1: command_1.flags.string({
+    bed1: core_1.Flags.string({
         description: 'Used only for mcscan anchors/simpleAnchors types',
     }),
-    bed2: command_1.flags.string({
+    bed2: core_1.Flags.string({
         description: 'Used only for mcscan anchors/simpleAnchors types',
     }),
 };

package/lib/commands/admin-server.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const command_1 = require("@oclif/command");
+const core_1 = require("@oclif/core");
 const path_1 = __importDefault(require("path"));
 const fs_1 = __importDefault(require("fs"));
 const crypto_1 = __importDefault(require("crypto"));
@@ -22,7 +22,7 @@ function generateKey() {
 }
 class AdminServer extends base_1.default {
     async run() {
-        const { flags: runFlags } = this.parse(AdminServer);
+        const { flags: runFlags } = await this.parse(AdminServer);
         const { root, bodySizeLimit } = runFlags;
         const output = root || '.';
         const isDir = fs_1.default.lstatSync(output).isDirectory();
@@ -67,7 +67,7 @@ class AdminServer extends base_1.default {
                     const filename = req.body.configPath
                         ? path_1.default.join(baseDir, req.body.configPath)
                         : outFile;
-                    if (filename.indexOf(baseDir) !== 0) {
+                    if (!filename.startsWith(baseDir)) {
                         throw new Error(`Cannot perform directory traversal outside of ${baseDir}`);
                     }
                     await this.writeJsonFile(filename, req.body.config);
@@ -126,18 +126,18 @@ class AdminServer extends base_1.default {
 AdminServer.description = 'Start up a small admin server for JBrowse configuration';
 AdminServer.examples = ['$ jbrowse admin-server', '$ jbrowse admin-server -p 8888'];
 AdminServer.flags = {
-    port: command_1.flags.string({
+    port: core_1.Flags.string({
         char: 'p',
         description: 'Specifified port to start the server on;\nDefault is 9090.',
     }),
-    root: command_1.flags.string({
+    root: core_1.Flags.string({
         description: 'path to the root of the JB2 installation.\nCreates ./config.json if nonexistent. note that you can navigate to ?config=path/to/subconfig.json in the web browser and it will write to rootDir/path/to/subconfig.json',
     }),
-    bodySizeLimit: command_1.flags.string({
+    bodySizeLimit: core_1.Flags.string({
         description: 'Size limit of the update message; may need to increase if config is large.\nArgument is passed to bytes library for parsing: https://www.npmjs.com/package/bytes.',
         default: '25mb',
     }),
-    help: command_1.flags.help({ char: 'h' }),
+    help: core_1.Flags.help({ char: 'h' }),
 };
 exports.default = AdminServer;
 function getNetworkAddress() {

package/lib/commands/create.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const command_1 = require("@oclif/command");
+const core_1 = require("@oclif/core");
 const fs_1 = __importDefault(require("fs"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
@@ -11,7 +11,7 @@ const decompress_1 = __importDefault(require("decompress"));
 const fsPromises = fs_1.default.promises;
 class Create extends base_1.default {
     async run() {
-        const { args: runArgs, flags: runFlags } = this.parse(Create);
+        const { args: runArgs, flags: runFlags } = await this.parse(Create);
         const { localPath: argsPath } = runArgs;
         this.debug(`Want to install path at: ${argsPath}`);
         const { force, url, listVersions, tag, branch, nightly } = runFlags;
@@ -50,9 +50,8 @@ class Create extends base_1.default {
         }
     }
     async catch(error) {
-        var _a;
         // @ts-expect-error
-        if ((_a = error.parse) === null || _a === void 0 ? void 0 : _a.output.flags.listVersions) {
+        if (error.parse?.output.flags.listVersions) {
             const versions = (await this.fetchGithubVersions()).map(version => version.tag_name);
             this.log(`All JBrowse versions:\n${versions.join('\n')}`);
             this.exit();
@@ -77,35 +76,34 @@ Create.examples = [
     '# List available versions',
     '$ jbrowse create --listVersions',
 ];
-Create.args = [
-    {
-        name: 'localPath',
+Create.args = {
+    localPath: core_1.Args.string({
         required: true,
         description: `Location where JBrowse 2 will be installed`,
-    },
-];
+    }),
+};
 Create.flags = {
-    help: command_1.flags.help({ char: 'h' }),
-    force: command_1.flags.boolean({
+    help: core_1.Flags.help({ char: 'h' }),
+    force: core_1.Flags.boolean({
         char: 'f',
         description: 'Overwrites existing JBrowse 2 installation if present in path',
     }),
     // will need to account for pagenation once there is a lot of releases
-    listVersions: command_1.flags.boolean({
+    listVersions: core_1.Flags.boolean({
         char: 'l',
         description: 'Lists out all versions of JBrowse 2',
     }),
-    branch: command_1.flags.string({
+    branch: core_1.Flags.string({
         description: 'Download a development build from a named git branch',
     }),
-    nightly: command_1.flags.boolean({
+    nightly: core_1.Flags.boolean({
         description: 'Download the latest development build from the main branch',
     }),
-    url: command_1.flags.string({
+    url: core_1.Flags.string({
         char: 'u',
         description: 'A direct URL to a JBrowse 2 release',
     }),
-    tag: command_1.flags.string({
+    tag: core_1.Flags.string({
         char: 't',
         description: 'Version of JBrowse 2 to install. Format is v1.0.0.\nDefaults to latest',
     }),

package/lib/commands/remove-track.js

@@ -3,36 +3,34 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const command_1 = require("@oclif/command");
+const core_1 = require("@oclif/core");
 const fs_1 = require("fs");
 const base_1 = __importDefault(require("../base"));
 class RemoveTrackJson extends base_1.default {
     async run() {
-        var _a;
-        const { args, flags: runFlags } = this.parse(RemoveTrackJson);
+        const { args, flags: runFlags } = await this.parse(RemoveTrackJson);
         const output = runFlags.target || runFlags.out || '.';
         const isDir = (await fs_1.promises.lstat(output)).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
         const { track: inputId } = args;
         const config = await this.readJsonFile(this.target);
-        config.tracks = (_a = config.tracks) === null || _a === void 0 ? void 0 : _a.filter(({ trackId }) => trackId !== inputId);
+        config.tracks = config.tracks?.filter(({ trackId }) => trackId !== inputId);
         await this.writeJsonFile(this.target, config);
     }
 }
 RemoveTrackJson.description = 'Remove a track configuration from a JBrowse 2 configuration. Be aware that this can cause crashes in saved sessions that refer to this track!';
 RemoveTrackJson.examples = ['$ jbrowse remove-track-json trackId'];
-RemoveTrackJson.args = [
-    {
-        name: 'track',
+RemoveTrackJson.args = {
+    track: core_1.Args.string({
         required: true,
         description: `track JSON file or command line arg blob`,
-    },
-];
+    }),
+};
 RemoveTrackJson.flags = {
-    target: command_1.flags.string({
+    target: core_1.Flags.string({
         description: 'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',
     }),
-    out: command_1.flags.string({
+    out: core_1.Flags.string({
         description: 'synonym for target',
     }),
 };