@jbrowse/cli 2.6.2 → 2.7.0

package/bin/dev

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

package/bin/dev.cmd

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

package/bin/run

@@ -1,5 +1,8 @@
 #!/usr/bin/env node
 
-require('@oclif/command').run()
-.then(require('@oclif/command/flush'))
-.catch(require('@oclif/errors/handle'))
+const oclif = require('@oclif/core')
+
+oclif
+  .run()
+  .then(require('@oclif/core/flush'))
+  .catch(require('@oclif/core/handle'))

package/lib/base.js

@@ -2,35 +2,16 @@
 /**
  * By convention, exit codes in this base class are below 100
  */
-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 __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
-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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const command_1 = __importDefault(require("@oclif/command"));
+const core_1 = require("@oclif/core");
 const fs_1 = require("fs");
 const path_1 = __importDefault(require("path"));
 const json_parse_better_errors_1 = __importDefault(require("json-parse-better-errors"));
 const fetchWithProxy_1 = __importDefault(require("./fetchWithProxy"));
-class JBrowseCommand extends command_1.default {
+class JBrowseCommand extends core_1.Command {
     async init() { }
     async readFile(location) {
         return fs_1.promises.readFile(location, { encoding: 'utf8' });
@@ -115,80 +96,51 @@ class JBrowseCommand extends command_1.default {
         return result;
     }
     async fetchGithubVersions() {
-        var _a, e_1, _b, _c;
         let versions = [];
-        try {
-            for (var _d = true, _e = __asyncValues(this.fetchVersions()), _f; _f = await _e.next(), _a = _f.done, !_a; _d = true) {
-                _c = _f.value;
-                _d = false;
-                const iter = _c;
-                versions = [...versions, ...iter];
-            }
-        }
-        catch (e_1_1) { e_1 = { error: e_1_1 }; }
-        finally {
-            try {
-                if (!_d && !_a && (_b = _e.return)) await _b.call(_e);
-            }
-            finally { if (e_1) throw e_1.error; }
+        for await (const iter of this.fetchVersions()) {
+            versions = [...versions, ...iter];
         }
         return versions;
     }
     async getLatest() {
-        var _a, e_2, _b, _c;
-        var _d;
-        try {
-            for (var _e = true, _f = __asyncValues(this.fetchVersions()), _g; _g = await _f.next(), _a = _g.done, !_a; _e = true) {
-                _c = _g.value;
-                _e = false;
-                const versions = _c;
-                // if a release was just uploaded, or an erroneous build was made
-                // then it might have no build asset
-                const nonprereleases = versions
-                    .filter(release => release.prerelease === false)
-                    .filter(release => release.assets && release.assets.length > 0);
-                if (nonprereleases.length > 0) {
-                    // @ts-expect-error
-                    const file = (_d = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))) === null || _d === void 0 ? void 0 : _d.browser_download_url;
-                    if (!file) {
-                        throw new Error('no jbrowse-web download found');
-                    }
-                    return file;
+        for await (const versions of this.fetchVersions()) {
+            // if a release was just uploaded, or an erroneous build was made
+            // then it might have no build asset
+            const nonprereleases = versions
+                .filter(release => release.prerelease === false)
+                .filter(release => release.assets && release.assets.length > 0);
+            if (nonprereleases.length > 0) {
+                // @ts-expect-error
+                const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
+                if (!file) {
+                    throw new Error('no jbrowse-web download found');
                 }
+                return file;
             }
         }
-        catch (e_2_1) { e_2 = { error: e_2_1 }; }
-        finally {
-            try {
-                if (!_e && !_a && (_b = _f.return)) await _b.call(_f);
-            }
-            finally { if (e_2) throw e_2.error; }
-        }
         throw new Error('no version tags found');
     }
-    fetchVersions() {
-        return __asyncGenerator(this, arguments, function* fetchVersions_1() {
-            let page = 1;
-            let result;
-            do {
-                const response = yield __await((0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`));
-                if (response.ok) {
-                    result = (yield __await(response.json()));
-                    yield yield __await(result.filter(release => release.tag_name.startsWith('v')));
-                    page++;
-                }
-                else {
-                    throw new Error(`${response.statusText}`);
-                }
-            } while (result && result.length > 0);
-        });
+    async *fetchVersions() {
+        let page = 1;
+        let result;
+        do {
+            const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`);
+            if (response.ok) {
+                result = (await response.json());
+                yield result.filter(release => release.tag_name.startsWith('v'));
+                page++;
+            }
+            else {
+                throw new Error(`${response.statusText}`);
+            }
+        } while (result && result.length > 0);
     }
     async getTag(tag) {
-        var _a, _b;
         const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
         if (response.ok) {
             const result = (await response.json());
-            const file = (_b = (_a = result === null || result === void 0 ? void 0 : result.assets) === null || _a === void 0 ? void 0 : _a.find(f => f.name.includes('jbrowse-web'))) === null || _b === void 0 ? void 0 : _b.browser_download_url;
+            const file = result?.assets?.find(f => f.name.includes('jbrowse-web'))
+                ?.browser_download_url;
             if (!file) {
                 this.error('Could not find version specified. Use --listVersions to see all available versions', { exit: 90 });
             }

package/lib/commands/add-assembly.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 base_1 = __importDefault(require("../base"));
@@ -20,7 +20,7 @@ function isValidJSON(string) {
 class AddAssembly extends base_1.default {
     async getAssembly() {
         let sequence;
-        const { args: runArgs, flags: runFlags } = this.parse(AddAssembly);
+        const { args: runArgs, flags: runFlags } = await this.parse(AddAssembly);
         const { sequence: argsSequence } = runArgs;
         if (this.needLoadData(argsSequence) && !runFlags.load) {
             this.error(`Please specify the loading operation for this file with --load copy|symlink|move|inPlace`, { exit: 110 });
@@ -193,7 +193,7 @@ class AddAssembly extends base_1.default {
     async run() {
         // https://stackoverflow.com/a/35008327/2129219
         const exists = (s) => new Promise(r => fs_1.default.access(s, fs_1.default.constants.F_OK, e => r(!e)));
-        const { args: runArgs, flags: runFlags } = this.parse(AddAssembly);
+        const { args: runArgs, flags: runFlags } = await this.parse(AddAssembly);
         const output = runFlags.target || runFlags.out || '.';
         if (!(await exists(output))) {
             const dir = output.endsWith('.json') ? path_1.default.dirname(output) : output;
@@ -209,7 +209,7 @@ class AddAssembly extends base_1.default {
         this.debug(`Sequence location is: ${argsSequence}`);
         const { name } = runFlags;
         const assembly = await this.getAssembly();
-        if (runFlags.alias && runFlags.alias.length) {
+        if (runFlags.alias?.length) {
             this.debug(`Adding assembly aliases: ${runFlags.alias}`);
             assembly.aliases = runFlags.alias;
         }
@@ -261,11 +261,14 @@ class AddAssembly extends base_1.default {
         let configContents;
         if (fs_1.default.existsSync(this.target)) {
             this.debug(`Found existing config file ${this.target}`);
-            configContents = Object.assign(Object.assign({}, defaultConfig), (await this.readJsonFile(this.target)));
+            configContents = {
+                ...defaultConfig,
+                ...(await this.readJsonFile(this.target)),
+            };
         }
         else {
             this.debug(`Creating config file ${this.target}`);
-            configContents = Object.assign({}, defaultConfig);
+            configContents = { ...defaultConfig };
         }
         if (!configContents.assemblies) {
             configContents.assemblies = [];
@@ -399,9 +402,8 @@ AddAssembly.examples = [
     '# add a bgzip indexed fasta inferred by fa.gz extension. assumes .fa.gz.gzi and .fa.gz.fai files also exists',
     '$ jbrowse add-assembly myfile.fa.gz --load copy',
 ];
-AddAssembly.args = [
-    {
-        name: 'sequence',
+AddAssembly.args = {
+    sequence: core_1.Args.string({
         required: true,
         description: `sequence file or URL
 
@@ -409,10 +411,10 @@ If TYPE is indexedFasta or bgzipFasta, the index file defaults to <location>.fai
 and can be optionally specified with --faiLocation
 If TYPE is bgzipFasta, the gzip index file defaults to <location>.gzi and can be
 optionally specified with --gziLocation`,
-    },
-];
+    }),
+};
 AddAssembly.flags = {
-    type: command_1.flags.string({
+    type: core_1.Flags.string({
         char: 't',
         description: `type of sequence, by default inferred from sequence file
 
@@ -430,54 +432,54 @@ custom         Either a JSON file location or inline JSON that defines a custom
                sequence adapter; must provide --name if using inline JSON`,
         options: ['indexedFasta', 'bgzipFasta', 'twoBit', 'chromSizes', 'custom'],
     }),
-    name: command_1.flags.string({
+    name: core_1.Flags.string({
         char: 'n',
         description: 'Name of the assembly; if not specified, will be guessed using the sequence file name',
     }),
-    alias: command_1.flags.string({
+    alias: core_1.Flags.string({
         char: 'a',
         description: 'An alias for the assembly name (e.g. "hg38" if the name of the assembly is "GRCh38");\ncan be specified multiple times',
         multiple: true,
     }),
-    displayName: command_1.flags.string({
+    displayName: core_1.Flags.string({
         description: 'The display name to specify for the assembly, e.g. "Homo sapiens (hg38)" while the name can be a shorter identifier like "hg38"',
     }),
-    faiLocation: command_1.flags.string({
+    faiLocation: core_1.Flags.string({
         description: '[default: <fastaLocation>.fai] FASTA index file or URL',
     }),
-    gziLocation: command_1.flags.string({
+    gziLocation: core_1.Flags.string({
         description: '[default: <fastaLocation>.gzi] FASTA gzip index file or URL',
     }),
-    refNameAliases: command_1.flags.string({
+    refNameAliases: core_1.Flags.string({
         description: 'Reference sequence name aliases file or URL; assumed to be a tab-separated aliases\nfile unless --refNameAliasesType is specified',
     }),
-    refNameAliasesType: command_1.flags.string({
+    refNameAliasesType: core_1.Flags.string({
         description: 'Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either\na JSON file location or inline JSON that defines a custom sequence adapter',
         options: ['aliases', 'custom'],
         dependsOn: ['refNameAliases'],
     }),
-    refNameColors: command_1.flags.string({
+    refNameColors: core_1.Flags.string({
         description: 'A comma-separated list of color strings for the reference sequence names; will cycle\nthrough colors if there are fewer colors than sequences',
     }),
-    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',
     }),
-    help: command_1.flags.help({ char: 'h' }),
-    load: command_1.flags.string({
+    help: core_1.Flags.help({ char: 'h' }),
+    load: core_1.Flags.string({
         char: 'l',
         description: 'Required flag when using a local file. Choose how to manage the data directory. Copy, symlink, or move the data directory to the JBrowse directory. Or use inPlace to modify the config without doing any file operations',
         options: ['copy', 'symlink', 'move', 'inPlace'],
     }),
-    skipCheck: command_1.flags.boolean({
+    skipCheck: core_1.Flags.boolean({
         description: "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory",
     }),
-    overwrite: command_1.flags.boolean({
+    overwrite: core_1.Flags.boolean({
         description: 'Overwrite existing assembly if one with the same name exists',
     }),
-    force: command_1.flags.boolean({
+    force: core_1.Flags.boolean({
         char: 'f',
         description: 'Equivalent to `--skipCheck --overwrite`',
     }),

package/lib/commands/add-connection.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"));
@@ -12,8 +12,7 @@ const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 const base_1 = __importDefault(require("../base"));
 class AddConnection extends base_1.default {
     async run() {
-        var _a, _b;
-        const { args: runArgs, flags: runFlags } = this.parse(AddConnection);
+        const { args: runArgs, flags: runFlags } = await this.parse(AddConnection);
         const output = runFlags.target || runFlags.out || '.';
         const isDir = fs_1.default.lstatSync(output).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
@@ -23,29 +22,37 @@ class AddConnection extends base_1.default {
         const url = await this.resolveURL(connectionUrlOrPath, !(skipCheck || force));
         const configContents = await this.readJsonFile(this.target);
         this.debug(`Using config file ${this.target}`);
-        if (!((_a = configContents.assemblies) === null || _a === void 0 ? void 0 : _a.length)) {
+        if (!configContents.assemblies?.length) {
             this.error('No assemblies found. Please add one before adding connections', { exit: 120 });
         }
         const configType = type || this.determineConnectionType(url);
         const id = connectionId ||
             [configType, assemblyNames, +Date.now()].filter(f => !!f).join('-');
-        const connectionConfig = Object.assign(Object.assign(Object.assign(Object.assign({ type: configType, name: name || id }, (configType === 'UCSCTrackHubConnection'
-            ? {
-                hubTxtLocation: {
-                    uri: url,
-                    locationType: 'UriLocation',
-                },
-            }
-            : {})), (configType === 'JBrowse1Connection'
-            ? {
-                dataDirLocation: {
-                    uri: url,
-                    locationType: 'UriLocation',
-                },
-            }
-            : {})), { connectionId: id, assemblyNames: assemblyNames || type === 'JBrowse1Connection'
-                ? [(_b = configContents.assemblies[0]) === null || _b === void 0 ? void 0 : _b.name]
-                : undefined }), (config ? (0, json_parse_better_errors_1.default)(config) : {}));
+        const connectionConfig = {
+            type: configType,
+            name: name || id,
+            ...(configType === 'UCSCTrackHubConnection'
+                ? {
+                    hubTxtLocation: {
+                        uri: url,
+                        locationType: 'UriLocation',
+                    },
+                }
+                : {}),
+            ...(configType === 'JBrowse1Connection'
+                ? {
+                    dataDirLocation: {
+                        uri: url,
+                        locationType: 'UriLocation',
+                    },
+                }
+                : {}),
+            connectionId: id,
+            assemblyNames: assemblyNames || type === 'JBrowse1Connection'
+                ? [configContents.assemblies[0]?.name]
+                : undefined,
+            ...(config ? (0, json_parse_better_errors_1.default)(config) : {}),
+        };
         if (!configContents.connections) {
             configContents.connections = [];
         }
@@ -121,47 +128,46 @@ AddConnection.examples = [
     `$ jbrowse add-connection http://mysite.com/path/to/custom --type custom --config '{"uri":{"url":"https://mysite.com/path/to/custom"}, "locationType": "UriLocation"}' -a hg19`,
     '$ jbrowse add-connection https://mysite.com/path/to/hub.txt --connectionId newId --name newName --target /path/to/jb2/installation/config.json',
 ];
-AddConnection.args = [
-    {
-        name: 'connectionUrlOrPath',
+AddConnection.args = {
+    connectionUrlOrPath: core_1.Args.string({
         required: true,
         description: `URL of data directory\nFor hub file, usually called hub.txt\nFor JBrowse 1, location of JB1 data directory similar to http://mysite.com/jbrowse/data/ `,
-    },
-];
+    }),
+};
 AddConnection.flags = {
-    type: command_1.flags.string({
+    type: core_1.Flags.string({
         char: 't',
         description: 'type of connection, ex. JBrowse1Connection, UCSCTrackHubConnection, custom',
     }),
-    assemblyNames: command_1.flags.string({
+    assemblyNames: core_1.Flags.string({
         char: 'a',
         description: 'For UCSC, optional: Comma separated list of assembly name(s) to filter from this connection. For JBrowse: a single assembly name',
     }),
-    config: command_1.flags.string({
+    config: core_1.Flags.string({
         char: 'c',
         description: `Any extra config settings to add to connection in JSON object format, such as '{"uri":"url":"https://sample.com"}, "locationType": "UriLocation"}'`,
     }),
-    connectionId: command_1.flags.string({
+    connectionId: core_1.Flags.string({
         description: `Id for the connection that must be unique to JBrowse.  Defaults to 'connectionType-assemblyName-currentTime'`,
     }),
-    name: command_1.flags.string({
+    name: core_1.Flags.string({
         char: 'n',
         description: 'Name of the connection. Defaults to connectionId if not provided',
     }),
-    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',
     }),
-    help: command_1.flags.help({ char: 'h' }),
-    skipCheck: command_1.flags.boolean({
+    help: core_1.Flags.help({ char: 'h' }),
+    skipCheck: core_1.Flags.boolean({
         description: "Don't check whether or not the data directory URL exists or if you are in a JBrowse directory",
     }),
-    overwrite: command_1.flags.boolean({
+    overwrite: core_1.Flags.boolean({
         description: 'Overwrites any existing connections if same connection id',
     }),
-    force: command_1.flags.boolean({
+    force: core_1.Flags.boolean({
         char: 'f',
         description: 'Equivalent to `--skipCheck --overwrite`',
     }),

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

@@ -3,12 +3,12 @@ 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 AddTrackJson extends base_1.default {
     async run() {
-        const { args, flags: runFlags } = this.parse(AddTrackJson);
+        const { args, flags: runFlags } = await this.parse(AddTrackJson);
         const output = runFlags.target || runFlags.out || '.';
         const isDir = (await fs_1.promises.lstat(output)).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
@@ -46,22 +46,21 @@ AddTrackJson.examples = [
     '$ jbrowse add-track-json track.json',
     '$ jbrowse add-track-json track.json --update',
 ];
-AddTrackJson.args = [
-    {
-        name: 'track',
+AddTrackJson.args = {
+    track: core_1.Args.string({
         required: true,
         description: `track JSON file or command line arg blob`,
-    },
-];
+    }),
+};
 AddTrackJson.flags = {
-    update: command_1.flags.boolean({
+    update: core_1.Flags.boolean({
         char: 'u',
         description: `update the contents of an existing track, matched based on trackId`,
     }),
-    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',
     }),
 };