@jbrowse/cli 2.6.2 → 2.7.0

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

@@ -3,15 +3,14 @@ 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 json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
 const base_1 = __importDefault(require("../base"));
 const fsPromises = fs_1.default.promises;
 class SetDefaultSession extends base_1.default {
     async run() {
-        var _a;
-        const { flags: runFlags } = this.parse(SetDefaultSession);
+        const { flags: runFlags } = await this.parse(SetDefaultSession);
         const { session, name, tracks, currentSession, view, viewId, delete: deleteDefaultSession, } = runFlags;
         const output = runFlags.target || runFlags.out || '.';
         const isDir = (await fsPromises.lstat(output)).isDirectory();
@@ -30,7 +29,7 @@ class SetDefaultSession extends base_1.default {
             this.exit();
         }
         const foundTracks = [];
-        const existingDefaultSession = ((_a = configContents.defaultSession) === null || _a === void 0 ? void 0 : _a.length) > 0;
+        const existingDefaultSession = configContents.defaultSession?.length > 0;
         // must provide default session, or view, or tracks + view
         if (!session && !view && !tracks) {
             this.error(`No default session information provided, Please either provide a default session file or enter information to build a default session`, { exit: 120 });
@@ -49,9 +48,8 @@ class SetDefaultSession extends base_1.default {
                 }
                 trackIds = tracks.split(',').map(c => c.trim());
                 trackIds.forEach(trackId => {
-                    var _a;
                     this.log(trackId);
-                    const matchingTrack = (_a = configContents.tracks) === null || _a === void 0 ? void 0 : _a.find(track => trackId === track.trackId);
+                    const matchingTrack = configContents.tracks?.find(track => trackId === track.trackId);
                     if (!matchingTrack) {
                         this.error(`Track ${trackId} has not been added to config yet.\nPlease add the track with the add-track command before adding to the default session`, { exit: 140 });
                     }
@@ -108,42 +106,41 @@ SetDefaultSession.examples = [
     '$ jbrowse set-default-session --view LinearGenomeView, --name newName --viewId view-no-tracks',
     '$ jbrowse set-default-session --currentSession # Prints out current default session',
 ];
-SetDefaultSession.args = [];
 SetDefaultSession.flags = {
-    session: command_1.flags.string({
+    session: core_1.Flags.string({
         char: 's',
         description: 'set path to a file containing session in json format',
     }),
-    name: command_1.flags.string({
+    name: core_1.Flags.string({
         char: 'n',
         description: 'Give a name for the default session',
         default: 'New Default Session',
     }),
-    view: command_1.flags.string({
+    view: core_1.Flags.string({
         char: 'v',
         description: 'View type in config to be added as default session, i.e LinearGenomeView, CircularView, DotplotView.\nMust be provided if no default session file provided',
     }),
-    viewId: command_1.flags.string({
+    viewId: core_1.Flags.string({
         description: 'Identifier for the view. Will be generated on default',
     }),
-    tracks: command_1.flags.string({
+    tracks: core_1.Flags.string({
         char: 't',
         description: 'Track id or track ids as comma separated string to put into default session',
     }),
-    currentSession: command_1.flags.boolean({
+    currentSession: core_1.Flags.boolean({
         char: 'c',
         description: 'List out the current default session',
     }),
-    target: command_1.flags.string({
+    target: core_1.Flags.string({
         description: 'path to config file in JB2 installation directory to write out to',
     }),
-    out: command_1.flags.string({
+    out: core_1.Flags.string({
         description: 'synonym for target',
     }),
-    delete: command_1.flags.boolean({
+    delete: core_1.Flags.boolean({
         description: 'Delete any existing default session.',
     }),
-    help: command_1.flags.help({
+    help: core_1.Flags.help({
         char: 'h',
     }),
 };

package/lib/commands/text-index.js

@@ -1,28 +1,4 @@
 "use strict";
-var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-var __asyncValues = (this && this.__asyncValues) || function (o) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var m = o[Symbol.asyncIterator], i;
-    return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
-    function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
-    function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
-};
-var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
-    var i, p;
-    return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
-    function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: false } : f ? f(v) : v; } : f; }
-};
-var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
-    if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
-    var g = generator.apply(thisArg, _arguments || []), i, q = [];
-    return i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i;
-    function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }
-    function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
-    function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
-    function fulfill(value) { resume("next", value); }
-    function reject(value) { resume("throw", value); }
-    function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -31,7 +7,7 @@ const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const stream_1 = require("stream");
 const ixixx_1 = require("ixixx");
-const command_1 = require("@oclif/command");
+const core_1 = require("@oclif/core");
 // locals
 const gff3Adapter_1 = require("../types/gff3Adapter");
 const vcfAdapter_1 = require("../types/vcfAdapter");
@@ -48,7 +24,7 @@ function getLoc(elt) {
 }
 class TextIndex extends base_1.default {
     async run() {
-        const { flags } = this.parse(TextIndex);
+        const { flags } = await this.parse(TextIndex);
         const { perTrack, file } = flags;
         if (file) {
             await this.indexFileList();
@@ -62,8 +38,7 @@ class TextIndex extends base_1.default {
         this.log('Finished!');
     }
     async aggregateIndex() {
-        var _a;
-        const { flags } = this.parse(TextIndex);
+        const { flags } = await this.parse(TextIndex);
         const { out, target, tracks, assemblies, attributes, quiet, force, exclude, dryrun, prefixSize, } = flags;
         const outFlag = target || out || '.';
         const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
@@ -75,14 +50,14 @@ class TextIndex extends base_1.default {
             fs_1.default.mkdirSync(trixDir);
         }
         const aggregateTextSearchAdapters = config.aggregateTextSearchAdapters || [];
-        const asms = (assemblies === null || assemblies === void 0 ? void 0 : assemblies.split(',')) ||
-            ((_a = config.assemblies) === null || _a === void 0 ? void 0 : _a.map(a => a.name)) ||
+        const asms = assemblies?.split(',') ||
+            config.assemblies?.map(a => a.name) ||
             (config.assembly ? [config.assembly.name] : []);
-        if (!(asms === null || asms === void 0 ? void 0 : asms.length)) {
+        if (!asms?.length) {
             throw new Error('No assemblies found');
         }
         for (const asm of asms) {
-            const trackConfigs = await this.getTrackConfigs(confPath, tracks === null || tracks === void 0 ? void 0 : tracks.split(','), asm);
+            const trackConfigs = await this.getTrackConfigs(confPath, tracks?.split(','), asm);
             if (!trackConfigs.length) {
                 this.log('Indexing assembly ' + asm + '...(no tracks found)...');
                 continue;
@@ -134,11 +109,14 @@ class TextIndex extends base_1.default {
             }
         }
         if (!dryrun) {
-            writeConf(Object.assign(Object.assign({}, config), { aggregateTextSearchAdapters }), confPath);
+            writeConf({
+                ...config,
+                aggregateTextSearchAdapters,
+            }, confPath);
         }
     }
     async perTrackIndex() {
-        const { flags } = this.parse(TextIndex);
+        const { flags } = await this.parse(TextIndex);
         const { out, target, tracks, assemblies, attributes, quiet, force, exclude, prefixSize, } = flags;
         const outFlag = target || out || '.';
         const isDir = fs_1.default.lstatSync(outFlag).isDirectory();
@@ -153,13 +131,13 @@ class TextIndex extends base_1.default {
         if (assemblies) {
             throw new Error(`Can't specify assemblies when indexing per track, remove assemblies flag to continue.`);
         }
-        const confs = await this.getTrackConfigs(confFilePath, tracks === null || tracks === void 0 ? void 0 : tracks.split(','));
+        const confs = await this.getTrackConfigs(confFilePath, tracks?.split(','));
         if (!confs.length) {
             throw new Error(`Tracks not found in config.json, please add track configurations before indexing.`);
         }
         for (const trackConfig of confs) {
             const { textSearching, trackId, assemblyNames } = trackConfig;
-            if ((textSearching === null || textSearching === void 0 ? void 0 : textSearching.textSearchAdapter) && !force) {
+            if (textSearching?.textSearchAdapter && !force) {
                 this.log(`Note: ${trackId} has already been indexed with this configuration, use --force to overwrite this track. Skipping for now`);
                 continue;
             }
@@ -174,11 +152,15 @@ class TextIndex extends base_1.default {
                 assemblyNames,
                 prefixSize,
             });
-            if (!(textSearching === null || textSearching === void 0 ? void 0 : textSearching.textSearchAdapter)) {
+            if (!textSearching?.textSearchAdapter) {
                 // modifies track with new text search adapter
                 const index = configTracks.findIndex(track => trackId === track.trackId);
                 if (index !== -1) {
-                    configTracks[index] = Object.assign(Object.assign({}, trackConfig), { textSearching: Object.assign(Object.assign({}, textSearching), { textSearchAdapter: {
+                    configTracks[index] = {
+                        ...trackConfig,
+                        textSearching: {
+                            ...textSearching,
+                            textSearchAdapter: {
                                 type: 'TrixTextSearchAdapter',
                                 textSearchAdapterId: trackId + '-index',
                                 ixFilePath: {
@@ -194,18 +176,23 @@ class TextIndex extends base_1.default {
                                     locationType: 'UriLocation',
                                 },
                                 assemblyNames: assemblyNames,
-                            } }) });
+                            },
+                        },
+                    };
                 }
                 else {
                     this.log("Error: can't find trackId");
                 }
             }
-            writeConf(Object.assign(Object.assign({}, config), { tracks: configTracks }), confFilePath);
+            writeConf({ ...config, tracks: configTracks }, confFilePath);
         }
     }
     async indexFileList() {
-        const { flags } = this.parse(TextIndex);
+        const { flags } = await this.parse(TextIndex);
         const { out, target, fileId, file, attributes, quiet, exclude, prefixSize, } = flags;
+        if (!file) {
+            throw new Error('Cannot index file list without files');
+        }
         const outFlag = target || out || '.';
         const trixDir = path_1.default.join(outFlag, 'trix');
         if (!fs_1.default.existsSync(trixDir)) {
@@ -214,7 +201,7 @@ class TextIndex extends base_1.default {
         const trackConfigs = file
             .map(file => (0, common_1.guessAdapterFromFileName)(file))
             .filter(fileConfig => (0, common_1.supported)(fileConfig.adapter.type));
-        if (fileId === null || fileId === void 0 ? void 0 : fileId.length) {
+        if (fileId?.length) {
             for (let i = 0; i < fileId.length; i++) {
                 trackConfigs[i].trackId = fileId[i];
             }
@@ -255,50 +242,48 @@ class TextIndex extends base_1.default {
         });
         return ixIxxStream;
     }
-    indexFiles({ trackConfigs, attributes, outLocation, quiet, typesToExclude, }) {
-        return __asyncGenerator(this, arguments, function* indexFiles_1() {
-            for (const config of trackConfigs) {
-                const { adapter, textSearching } = config;
-                const { type } = adapter;
-                const { indexingFeatureTypesToExclude = typesToExclude, indexingAttributes = attributes, } = textSearching || {};
-                let loc;
-                if (type === 'Gff3TabixAdapter') {
-                    loc = adapter.gffGzLocation;
-                }
-                else if (type === 'Gff3Adapter') {
-                    loc = adapter.gffLocation;
-                }
-                else if (type === 'VcfAdapter') {
-                    loc = adapter.vcfLocation;
-                }
-                else if (type === 'VcfTabixAdapter') {
-                    loc = adapter.vcfGzLocation;
-                }
-                if (!loc) {
-                    return yield __await(void 0);
-                }
-                if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
-                    yield __await(yield* __asyncDelegator(__asyncValues((0, gff3Adapter_1.indexGff3)({
-                        config,
-                        attributesToIndex: indexingAttributes,
-                        inLocation: getLoc(loc),
-                        outLocation,
-                        typesToExclude: indexingFeatureTypesToExclude,
-                        quiet,
-                    }))));
-                }
-                else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
-                    yield __await(yield* __asyncDelegator(__asyncValues((0, vcfAdapter_1.indexVcf)({
-                        config,
-                        attributesToIndex: indexingAttributes,
-                        inLocation: getLoc(loc),
-                        outLocation,
-                        typesToExclude: indexingFeatureTypesToExclude,
-                        quiet,
-                    }))));
-                }
+    async *indexFiles({ trackConfigs, attributes, outLocation, quiet, typesToExclude, }) {
+        for (const config of trackConfigs) {
+            const { adapter, textSearching } = config;
+            const { type } = adapter;
+            const { indexingFeatureTypesToExclude = typesToExclude, indexingAttributes = attributes, } = textSearching || {};
+            let loc;
+            if (type === 'Gff3TabixAdapter') {
+                loc = adapter.gffGzLocation;
             }
-        });
+            else if (type === 'Gff3Adapter') {
+                loc = adapter.gffLocation;
+            }
+            else if (type === 'VcfAdapter') {
+                loc = adapter.vcfLocation;
+            }
+            else if (type === 'VcfTabixAdapter') {
+                loc = adapter.vcfGzLocation;
+            }
+            if (!loc) {
+                return;
+            }
+            if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
+                yield* (0, gff3Adapter_1.indexGff3)({
+                    config,
+                    attributesToIndex: indexingAttributes,
+                    inLocation: getLoc(loc),
+                    outLocation,
+                    typesToExclude: indexingFeatureTypesToExclude,
+                    quiet,
+                });
+            }
+            else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
+                yield* (0, vcfAdapter_1.indexVcf)({
+                    config,
+                    attributesToIndex: indexingAttributes,
+                    inLocation: getLoc(loc),
+                    outLocation,
+                    typesToExclude: indexingFeatureTypesToExclude,
+                    quiet,
+                });
+            }
+        }
     }
     runIxIxx({ readStream, outLocation, name, prefixSize, }) {
         return (0, ixixx_1.ixIxxStream)(readStream, path_1.default.join(outLocation, 'trix', `${name}.ix`), path_1.default.join(outLocation, 'trix', `${name}.ixx`), prefixSize);
@@ -308,7 +293,7 @@ class TextIndex extends base_1.default {
         if (!tracks) {
             return [];
         }
-        const trackIdsToIndex = trackIds || (tracks === null || tracks === void 0 ? void 0 : tracks.map(track => track.trackId));
+        const trackIdsToIndex = trackIds || tracks?.map(track => track.trackId);
         return trackIdsToIndex
             .map(trackId => {
             const currentTrack = tracks.find(t => trackId === t.trackId);
@@ -317,7 +302,7 @@ class TextIndex extends base_1.default {
             }
             return currentTrack;
         })
-            .filter(track => { var _a; return (0, common_1.supported)((_a = track.adapter) === null || _a === void 0 ? void 0 : _a.type); })
+            .filter(track => (0, common_1.supported)(track.adapter?.type))
             .filter(track => assemblyName ? track.assemblyNames.includes(assemblyName) : true);
     }
 }
@@ -339,53 +324,53 @@ TextIndex.examples = [
     '$ jbrowse text-index --file myfile.gff3.gz --file myfile.vcfgz --out indexes',
 ];
 TextIndex.flags = {
-    help: command_1.flags.help({ char: 'h' }),
-    tracks: command_1.flags.string({
+    help: core_1.Flags.help({ char: 'h' }),
+    tracks: core_1.Flags.string({
         description: `Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks`,
     }),
-    target: command_1.flags.string({
+    target: core_1.Flags.string({
         description: 'Path to config file in JB2 installation directory to read from.',
     }),
-    out: command_1.flags.string({
+    out: core_1.Flags.string({
         description: 'Synonym for target',
     }),
-    attributes: command_1.flags.string({
+    attributes: core_1.Flags.string({
         description: 'Comma separated list of attributes to index',
         default: 'Name,ID',
     }),
-    assemblies: command_1.flags.string({
+    assemblies: core_1.Flags.string({
         char: 'a',
         description: 'Specify the assembl(ies) to create an index for. If unspecified, creates an index for each assembly in the config',
     }),
-    force: command_1.flags.boolean({
+    force: core_1.Flags.boolean({
         default: false,
         description: 'Overwrite previously existing indexes',
     }),
-    quiet: command_1.flags.boolean({
+    quiet: core_1.Flags.boolean({
         char: 'q',
         default: false,
         description: 'Hide the progress bars',
     }),
-    perTrack: command_1.flags.boolean({
+    perTrack: core_1.Flags.boolean({
         default: false,
         description: 'If set, creates an index per track',
     }),
-    exclude: command_1.flags.string({
+    exclude: core_1.Flags.string({
         description: 'Adds gene type to list of excluded types',
         default: 'CDS,exon',
     }),
-    prefixSize: command_1.flags.integer({
+    prefixSize: core_1.Flags.integer({
         description: 'Specify the prefix size for the ixx index. We attempt to automatically calculate this, but you can manually specify this too. If many genes have similar gene IDs e.g. Z000000001, Z000000002 the prefix size should be larger so that they get split into different bins',
     }),
-    file: command_1.flags.string({
+    file: core_1.Flags.string({
         description: 'File or files to index (can be used to create trix indexes for embedded component use cases not using a config.json for example)',
         multiple: true,
     }),
-    fileId: command_1.flags.string({
+    fileId: core_1.Flags.string({
         description: 'Set the trackId used for the indexes generated with the --file argument',
         multiple: true,
     }),
-    dryrun: command_1.flags.boolean({
+    dryrun: core_1.Flags.boolean({
         description: 'Just print out tracks that will be indexed by the process, without doing any indexing',
     }),
 };

package/lib/commands/upgrade.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 rimraf_1 = require("rimraf");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
@@ -12,7 +12,7 @@ const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
 class Upgrade extends base_1.default {
     async run() {
-        const { args: runArgs, flags: runFlags } = this.parse(Upgrade);
+        const { args: runArgs, flags: runFlags } = await this.parse(Upgrade);
         const { localPath: argsPath } = runArgs;
         const { clean, listVersions, tag, url, branch, nightly } = runFlags;
         if (listVersions) {
@@ -73,35 +73,34 @@ Upgrade.examples = [
     '# Get nightly release from main branch',
     '$ jbrowse upgrade --nightly',
 ];
-Upgrade.args = [
-    {
-        name: 'localPath',
+Upgrade.args = {
+    localPath: core_1.Args.string({
         required: false,
         description: `Location where JBrowse 2 is installed`,
         default: '.',
-    },
-];
+    }),
+};
 Upgrade.flags = {
-    help: command_1.flags.help({ char: 'h' }),
+    help: core_1.Flags.help({ char: 'h' }),
     // 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',
     }),
-    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',
     }),
-    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',
     }),
-    clean: command_1.flags.boolean({
+    clean: core_1.Flags.boolean({
         description: 'Removes old js,map,and LICENSE files in the installation',
     }),
-    url: command_1.flags.string({
+    url: core_1.Flags.string({
         char: 'u',
         description: 'A direct URL to a JBrowse 2 release',
     }),

package/lib/fetchWithProxy.js

@@ -9,6 +9,6 @@ const proxy_agent_1 = require("proxy-agent");
 // via the `http_proxy` / `https_proxy` / `no_proxy` / etc. env vars
 function fetchWithProxy(url, options = {}) {
     const agent = new proxy_agent_1.ProxyAgent();
-    return (0, node_fetch_1.default)(url, Object.assign({ agent }, options));
+    return (0, node_fetch_1.default)(url, { agent, ...options });
 }
 exports.default = fetchWithProxy;

package/lib/index.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.run = void 0;
-var command_1 = require("@oclif/command");
-Object.defineProperty(exports, "run", { enumerable: true, get: function () { return command_1.run; } });
+var core_1 = require("@oclif/core");
+Object.defineProperty(exports, "run", { enumerable: true, get: function () { return core_1.run; } });
 // trigger build

package/lib/types/common.js

@@ -117,8 +117,8 @@ exports.supported = supported;
 async function generateMeta({ trackConfigs, attributes, outLocation, name, typesToExclude, assemblyNames, }) {
     const tracks = trackConfigs.map(({ adapter, textSearching, trackId }) => ({
         trackId,
-        attributesIndexed: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingAttributes) || attributes,
-        excludedTypes: (textSearching === null || textSearching === void 0 ? void 0 : textSearching.indexingFeatureTypesToExclude) || typesToExclude,
+        attributesIndexed: textSearching?.indexingAttributes || attributes,
+        excludedTypes: textSearching?.indexingFeatureTypesToExclude || typesToExclude,
         adapterConf: adapter,
     }));
     fs_1.default.writeFileSync(path_1.default.join(outLocation, 'trix', `${name}_meta.json`), JSON.stringify({