@jbrowse/cli 1.4.4 → 1.5.3

package/lib/commands/add-track.d.ts

@@ -2,9 +2,11 @@ import { flags } from '@oclif/command';
 import JBrowseCommand from '../base';
 interface UriLocation {
     uri: string;
+    locationType: 'UriLocation';
 }
 interface LocalPathLocation {
     localPath: string;
+    locationType: 'LocalPathLocation';
 }
 export default class AddTrack extends JBrowseCommand {
     target: string;
@@ -40,21 +42,17 @@ export default class AddTrack extends JBrowseCommand {
         index: string;
         index2?: undefined;
     } | {
-        file?: undefined;
+        file: string;
         index?: undefined;
         index2?: undefined;
     } | {
-        file: string;
-        index: undefined;
+        file?: undefined;
+        index?: undefined;
         index2?: undefined;
     } | {
         file: string;
         index: string;
         index2: string;
-    } | {
-        file: string;
-        index?: undefined;
-        index2?: undefined;
     };
     guessAdapter(fileName: string, protocol: string, index?: string): {
         type: string;
@@ -65,7 +63,9 @@ export default class AddTrack extends JBrowseCommand {
         };
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -85,7 +85,9 @@ export default class AddTrack extends JBrowseCommand {
         craiLocation: UriLocation | LocalPathLocation;
         bamLocation?: undefined;
         index?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -101,11 +103,13 @@ export default class AddTrack extends JBrowseCommand {
         pafLocation?: undefined;
     } | {
         type: string;
+        gffLocation: UriLocation | LocalPathLocation;
         bamLocation?: undefined;
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -129,6 +133,30 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
+        bedGzLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+    } | {
+        type: string;
+        gtfLocation: UriLocation | LocalPathLocation;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -149,7 +177,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
         bigBedLocation?: undefined;
@@ -172,8 +202,32 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
+        gffGzLocation?: undefined;
+        gtfLocation?: undefined;
+        vcfLocation?: undefined;
+        bedGzLocation?: undefined;
+        bigBedLocation?: undefined;
+        bigWigLocation?: undefined;
+        fastaLocation?: undefined;
+        faiLocation?: undefined;
+        gziLocation?: undefined;
+        twoBitLocation?: undefined;
+        rootUrlTemplate?: undefined;
+        endpoint?: undefined;
+        hicLocation?: undefined;
+        pafLocation?: undefined;
+    } | {
+        type: string;
+        bamLocation?: undefined;
+        index?: undefined;
+        cramLocation?: undefined;
+        craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
+        vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
         bigBedLocation?: undefined;
         bigWigLocation?: undefined;
@@ -195,7 +249,9 @@ export default class AddTrack extends JBrowseCommand {
         bamLocation?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bigBedLocation?: undefined;
@@ -215,7 +271,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -235,7 +293,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -256,7 +316,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -277,7 +339,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -295,7 +359,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -315,7 +381,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -335,7 +403,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -355,7 +425,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;
@@ -375,7 +447,9 @@ export default class AddTrack extends JBrowseCommand {
         index?: undefined;
         cramLocation?: undefined;
         craiLocation?: undefined;
+        gffLocation?: undefined;
         gffGzLocation?: undefined;
+        gtfLocation?: undefined;
         vcfLocation?: undefined;
         vcfGzLocation?: undefined;
         bedGzLocation?: undefined;

package/lib/commands/add-track.js

@@ -2,18 +2,20 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const path_1 = tslib_1.__importDefault(require("path"));
-const json_parse_better_errors_1 = tslib_1.__importDefault(require("json-parse-better-errors"));
-const base_1 = tslib_1.__importDefault(require("../base"));
-const fsPromises = fs_1.default.promises;
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const json_parse_better_errors_1 = (0, tslib_1.__importDefault)(require("json-parse-better-errors"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
+const { copyFile, rename, symlink, lstat, unlink } = fs_1.default.promises;
+const { COPYFILE_EXCL } = fs_1.default.constants;
+const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
 class AddTrack extends base_1.default {
     async run() {
         const { args: runArgs, flags: runFlags } = this.parse(AddTrack);
         const { track: argsTrack } = runArgs;
         const { config, skipCheck, force, overwrite, category, description, load, subDir, target, protocol, out, indexFile: index, } = runFlags;
         const output = target || out || '.';
-        const isDir = (await fsPromises.lstat(output)).isDirectory();
+        const isDir = (await lstat(output)).isDirectory();
         this.target = isDir ? `${output}/config.json` : output;
         let { trackType, trackId, name, assemblyNames } = runFlags;
         const configDirectory = path_1.default.dirname(this.target);
@@ -27,7 +29,6 @@ class AddTrack extends base_1.default {
             }
         }
         const location = argsTrack;
-        const isUrl = (loc) => loc === null || loc === void 0 ? void 0 : loc.match(/^https?:\/\//);
         const inPlace = load === 'inPlace';
         const useIndex = isUrl(index) || inPlace || index;
         const effectiveLocation = isUrl(location) || inPlace
@@ -76,13 +77,11 @@ class AddTrack extends base_1.default {
         this.debug(`Type is: ${trackType}`);
         this.debug(`Track is :${trackId}`);
         this.debug(`Assembly name(s) is :${assemblyNames}`);
-        const configObj = config ? json_parse_better_errors_1.default(config) : {};
+        const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
         const trackConfig = Object.assign({ type: trackType, trackId,
-            name, category: category ? category.split(',').map(c => c.trim()) : undefined, assemblyNames: assemblyNames.split(',').map(a => a.trim()), adapter }, configObj);
+            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);
         this.debug(`Track location: ${location}, index: ${adapter ? adapter.index : ''}`);
-        if (description) {
-            trackConfig.description = description;
-        }
         // any special track modifications go here
         switch (trackType) {
             case 'AlignmentsTrack': {
@@ -113,56 +112,27 @@ class AddTrack extends base_1.default {
         else {
             configContents.tracks.push(trackConfig);
         }
-        // copy/symlinks/moves the track into the jbrowse installation directory
-        const filePaths = Object.values(this.guessFileNames(location, index)).filter(f => !!f);
-        const destinationFn = (dir, file) => path_1.default.join(dir, subDir, path_1.default.basename(file));
-        switch (load) {
-            case 'copy': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e);
-                    }
-                    return fsPromises.copyFile(filePath, dest, fs_1.default.constants.COPYFILE_EXCL);
-                }));
-                break;
-            }
-            case 'symlink': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e);
-                    }
-                    return fsPromises.symlink(filePath, dest);
-                }));
-                break;
+        const filePaths = Object.values(this.guessFileNames(location, index)).filter((f) => !!f);
+        // get path of destination, and remove file at that path if it exists and
+        // force is set
+        const destinationFn = async (dir, file) => {
+            const dest = path_1.default.join(dir, subDir, path_1.default.basename(file));
+            if (force && fs_1.default.existsSync(dest)) {
+                await unlink(dest);
             }
-            case 'move': {
-                await Promise.all(filePaths.map(async (filePath) => {
-                    const dest = destinationFn(configDirectory, filePath);
-                    try {
-                        if (force && fs_1.default.existsSync(dest)) {
-                            await fsPromises.unlink(dest);
-                        }
-                    }
-                    catch (e) {
-                        this.error(e);
-                    }
-                    return fsPromises.rename(filePath, dest);
-                }));
-                break;
+            return dest;
+        };
+        const callbacks = {
+            copy: (src, dest) => copyFile(src, dest, COPYFILE_EXCL),
+            move: (src, dest) => rename(src, dest),
+            symlink: (src, dest) => symlink(src, dest),
+        };
+        await Promise.all(filePaths.map(async (src) => {
+            const dest = await destinationFn(configDirectory, src);
+            if (load === 'copy' || load === 'move' || load === 'symlink') {
+                return callbacks[load](src, dest);
             }
-        }
+        }));
         this.debug(`Writing configuration to file ${this.target}`);
         await this.writeJsonFile(this.target, configContents);
         this.log(`${idx !== -1 ? 'Overwrote' : 'Added'} track "${name}" ${idx !== -1 ? 'in' : 'to'} ${this.target}`);
@@ -177,28 +147,34 @@ class AddTrack extends base_1.default {
         if (/\.cram$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.crai`,
+                index: index || `${fileName}.crai`,
             };
         }
         if (/\.gff3?$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.gff3?\.b?gz$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.tbi`,
+                index: index || `${fileName}.tbi`,
             };
         }
         if (/\.gtf?$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.vcf$/i.test(fileName)) {
-            return {};
+            return {
+                file: fileName,
+            };
         }
         if (/\.vcf\.b?gz$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: `${fileName}.tbi`,
+                index: index || `${fileName}.tbi`,
             };
         }
         if (/\.vcf\.idx$/i.test(fileName)) {
@@ -219,13 +195,11 @@ class AddTrack extends base_1.default {
         if (/\.(bb|bigbed)$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: undefined,
             };
         }
         if (/\.(bw|bigwig)$/i.test(fileName)) {
             return {
                 file: fileName,
-                index: undefined,
             };
         }
         if (/\.(fa|fasta|fas|fna|mfa)$/i.test(fileName)) {
@@ -275,10 +249,13 @@ class AddTrack extends base_1.default {
     guessAdapter(fileName, protocol, index) {
         function makeLocation(location) {
             if (protocol === 'uri') {
-                return { uri: location };
+                return { uri: location, locationType: 'UriLocation' };
             }
             if (protocol === 'localPath') {
-                return { localPath: location };
+                return {
+                    localPath: location,
+                    locationType: 'LocalPathLocation',
+                };
             }
             throw new Error(`invalid protocol ${protocol}`);
         }
@@ -301,7 +278,8 @@ class AddTrack extends base_1.default {
         }
         if (/\.gff3?$/i.test(fileName)) {
             return {
-                type: 'UNSUPPORTED',
+                type: 'Gff3Adapter',
+                gffLocation: makeLocation(fileName),
             };
         }
         if (/\.gff3?\.b?gz$/i.test(fileName)) {
@@ -316,7 +294,8 @@ class AddTrack extends base_1.default {
         }
         if (/\.gtf?$/i.test(fileName)) {
             return {
-                type: 'UNSUPPORTED',
+                type: 'GtfAdapter',
+                gtfLocation: makeLocation(fileName),
             };
         }
         if (/\.vcf$/i.test(fileName)) {
@@ -439,18 +418,23 @@ class AddTrack extends base_1.default {
 exports.default = AddTrack;
 AddTrack.description = 'Add a track to a JBrowse 2 configuration';
 AddTrack.examples = [
-    `# --load copy copies my.bam and my.bam.bai to current directory and adds track to config.json`,
-    '$ jbrowse add-track /path/to/my.bam --load copy\n',
-    `# same as above, but specify path to bai file`,
-    '$ jbrowse add-track /path/to/my.bam --indexFile /path/to/my.bai --load copy\n',
-    `# --load symlink creates symlink in /path/to/jb2/ directory for this file, and adds track to config.json`,
-    '$ jbrowse add-track /path/to/my.bam --target /path/to/jb2/config.json --load symlink\n',
-    `# no --load flag to add literal URL for this track to config.json`,
-    '$ jbrowse add-track https://mywebsite.com/my.bam\n',
-    `# --load move to move the file `,
-    `$ jbrowse add-track /path/to/my.bam --name 'New Track' --load move\n`,
-    `# --load inPlace puts /url/relative/path.bam in the config without performing any file operations`,
-    `$ jbrowse add-track /url/relative/path.bam --trackId AlignmentsTrack1 --load url --overwrite`,
+    '# copy /path/to/my.bam and /path/to/my.bam.bai to current directory and adds track to config.json',
+    '$ jbrowse add-track /path/to/my.bam --load copy',
+    '',
+    '# copy my.bam and my.bam.bai to /path/to/jb2/bam and adds track entry to /path/to/jb2/bam/config.json',
+    '$ jbrowse add-track my.bam --load copy --out /path/to/jb2 --subDir bam',
+    '',
+    `# same as above, but specify path to bai file. needed for if the bai file does not have the extension .bam.bai`,
+    '$ jbrowse add-track my.bam --indexFile my.bai --load copy',
+    '',
+    '# creates symlink for /path/to/my.bam and adds track to config.json',
+    '$ jbrowse add-track /path/to/my.bam --load symlink',
+    '',
+    '# add track from URL to config.json, no --load flag needed',
+    '$ jbrowse add-track https://mywebsite.com/my.bam',
+    '',
+    '# --load inPlace adds a track without doing file operations',
+    '$ jbrowse add-track /url/relative/path.bam --load inPlace',
 ];
 AddTrack.args = [
     {

package/lib/commands/admin-server.d.ts

@@ -1,14 +1,12 @@
 import { flags } from '@oclif/command';
 import JBrowseCommand from '../base';
 export default class AdminServer extends JBrowseCommand {
-    private target;
     static description: string;
     static examples: string[];
     static flags: {
         port: flags.IOptionFlag<string | undefined>;
         target: flags.IOptionFlag<string | undefined>;
         out: flags.IOptionFlag<string | undefined>;
-        skipCheck: import("@oclif/parser/lib/flags").IBooleanFlag<boolean>;
         help: import("@oclif/parser/lib/flags").IBooleanFlag<void>;
     };
     run(): Promise<void>;

package/lib/commands/admin-server.js

@@ -2,15 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 const command_1 = require("@oclif/command");
-const fs_1 = tslib_1.__importDefault(require("fs"));
-const crypto_1 = tslib_1.__importDefault(require("crypto"));
-const boxen_1 = tslib_1.__importDefault(require("boxen"));
-const chalk_1 = tslib_1.__importDefault(require("chalk"));
-const os_1 = tslib_1.__importDefault(require("os"));
-const express_1 = tslib_1.__importDefault(require("express"));
-const cors_1 = tslib_1.__importDefault(require("cors"));
-const base_1 = tslib_1.__importDefault(require("../base"));
-const fsPromises = fs_1.default.promises;
+const path_1 = (0, tslib_1.__importDefault)(require("path"));
+const fs_1 = (0, tslib_1.__importDefault)(require("fs"));
+const crypto_1 = (0, tslib_1.__importDefault)(require("crypto"));
+const boxen_1 = (0, tslib_1.__importDefault)(require("boxen"));
+const chalk_1 = (0, tslib_1.__importDefault)(require("chalk"));
+const os_1 = (0, tslib_1.__importDefault)(require("os"));
+const express_1 = (0, tslib_1.__importDefault)(require("express"));
+const cors_1 = (0, tslib_1.__importDefault)(require("cors"));
+const base_1 = (0, tslib_1.__importDefault)(require("../base"));
 function isValidPort(port) {
     return port > 0 && port < 65535;
 }
@@ -21,25 +21,25 @@ function generateKey() {
 class AdminServer extends base_1.default {
     async run() {
         const { flags: runFlags } = this.parse(AdminServer);
-        const output = runFlags.target || runFlags.out || '.';
-        const isDir = (await fsPromises.lstat(output)).isDirectory();
-        this.target = isDir ? `${output}/config.json` : output;
-        // check if the config file exists, if none exists write default
-        const defaultConfig = {
-            assemblies: [],
-            configuration: {},
-            connections: [],
-            defaultSession: {
-                name: 'New Session',
-            },
-            tracks: [],
-        };
-        if (fs_1.default.existsSync(this.target)) {
-            this.debug(`Found existing config file ${this.target}`);
+        const { target, out } = runFlags;
+        const output = target || out || '.';
+        const isDir = fs_1.default.lstatSync(output).isDirectory();
+        const outFile = isDir ? `${output}/config.json` : output;
+        const baseDir = path_1.default.dirname(outFile);
+        if (fs_1.default.existsSync(outFile)) {
+            this.debug(`Found existing config file ${outFile}`);
         }
         else {
-            this.debug(`Creating config file ${this.target}`);
-            await this.writeJsonFile('./config.json', defaultConfig);
+            this.debug(`Creating config file ${outFile}`);
+            await this.writeJsonFile('./config.json', {
+                assemblies: [],
+                configuration: {},
+                connections: [],
+                defaultSession: {
+                    name: 'New Session',
+                },
+                tracks: [],
+            });
         }
         // start server with admin key in URL query string
         let port = 9090;
@@ -51,21 +51,28 @@ class AdminServer extends base_1.default {
                 port = parseInt(runFlags.port, 10);
             }
         }
-        const app = express_1.default();
+        const app = (0, express_1.default)();
         app.use(express_1.default.static('.'));
-        app.use(cors_1.default());
+        app.use((0, cors_1.default)());
         // POST route to save config
         app.use(express_1.default.json());
         app.post('/updateConfig', async (req, res) => {
-            this.debug('Req body: ', req.body);
-            if (req.body.adminKey === adminKey) {
+            if (adminKey === req.body.adminKey) {
                 this.debug('Admin key matches');
                 try {
-                    await this.writeJsonFile(this.target, req.body.config);
+                    // use directory traversal prevention
+                    // https://nodejs.org/en/knowledge/file-system/security/introduction/#preventing-directory-traversal
+                    const filename = req.body.configPath
+                        ? path_1.default.join(baseDir, req.body.configPath)
+                        : outFile;
+                    if (filename.indexOf(baseDir) !== 0) {
+                        throw new Error(`Cannot perform directory traversal outside of ${baseDir}`);
+                    }
+                    await this.writeJsonFile(filename, req.body.config);
                     res.send('Config written to disk');
                 }
-                catch (_a) {
-                    res.status(500).send('Could not write config file');
+                catch (e) {
+                    res.status(500).send(`Could not write config file ${e}`);
                 }
             }
             else {
@@ -110,7 +117,7 @@ class AdminServer extends base_1.default {
         if (networkAddress) {
             message += `\n${chalk_1.default.bold('- On Your Network:')}  ${networkAddress}`;
         }
-        this.log(boxen_1.default(message, { padding: 1, borderColor: 'blue', margin: 1 }));
+        this.log((0, boxen_1.default)(message, { padding: 1, borderColor: 'blue', margin: 1 }));
         this.log(`If you are running yarn start you can launch http://localhost:3000?adminKey=${adminKey}&adminServer=http://localhost:${port}/updateConfig`);
     }
 }
@@ -128,9 +135,6 @@ AdminServer.flags = {
     out: command_1.flags.string({
         description: 'synonym for target',
     }),
-    skipCheck: command_1.flags.boolean({
-        description: "Don't check whether or not you are in a JBrowse directory",
-    }),
     help: command_1.flags.help({ char: 'h' }),
 };
 function getNetworkAddress() {

package/lib/commands/create.d.ts

@@ -19,5 +19,5 @@ export default class Create extends JBrowseCommand {
     };
     run(): Promise<void>;
     checkPath(userPath: string): Promise<void>;
-    catch(error: any): Promise<void>;
+    catch(error: unknown): Promise<void>;
 }