@jbrowse/cli 2.13.1 → 2.14.0

package/README.md

@@ -205,7 +205,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/add-assembly.ts)_
+[src/commands/add-assembly.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/add-assembly.ts)_
 
 ## `jbrowse add-connection CONNECTIONURLORPATH`
 
@@ -256,7 +256,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/add-connection.ts)_
+[src/commands/add-connection.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/add-connection.ts)_
 
 ## `jbrowse add-track TRACK`
 
@@ -337,7 +337,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/add-track.ts)_
+[src/commands/add-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/add-track.ts)_
 
 ## `jbrowse add-track-json TRACK`
 
@@ -367,7 +367,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/add-track-json.ts)_
+[src/commands/add-track-json.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/add-track-json.ts)_
 
 ## `jbrowse admin-server`
 
@@ -399,7 +399,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/admin-server.ts)_
+[src/commands/admin-server.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/admin-server.ts)_
 
 ## `jbrowse create LOCALPATH`
 
@@ -456,7 +456,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/create.ts)_
+[src/commands/create.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/create.ts)_
 
 ## `jbrowse help [COMMAND]`
 
@@ -477,7 +477,7 @@ DESCRIPTION
 ```
 
 _See code:
-[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.7/src/commands/help.ts)_
+[@oclif/plugin-help](https://github.com/oclif/plugin-help/blob/v6.2.8/src/commands/help.ts)_
 
 ## `jbrowse make-pif FILE`
 
@@ -507,7 +507,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/make-pif.ts)_
+[src/commands/make-pif.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/make-pif.ts)_
 
 ## `jbrowse remove-track TRACK`
 
@@ -535,7 +535,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/remove-track.ts)_
+[src/commands/remove-track.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/remove-track.ts)_
 
 ## `jbrowse set-default-session`
 
@@ -577,7 +577,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/set-default-session.ts)_
+[src/commands/set-default-session.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/set-default-session.ts)_
 
 ## `jbrowse sort-gff FILE`
 
@@ -608,7 +608,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/sort-gff.ts)_
+[src/commands/sort-gff.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/sort-gff.ts)_
 
 ## `jbrowse text-index`
 
@@ -675,7 +675,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/text-index.ts)_
+[src/commands/text-index.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/text-index.ts)_
 
 ## `jbrowse upgrade [LOCALPATH]`
 
@@ -738,7 +738,7 @@ EXAMPLES
 ```
 
 _See code:
-[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.13.1/products/jbrowse-cli/src/commands/upgrade.ts)_
+[src/commands/upgrade.ts](https://github.com/GMOD/jbrowse-components/blob/v2.14.0/products/jbrowse-cli/src/commands/upgrade.ts)_
 
 <!-- commandsstop -->
 

package/lib/base.js

@@ -42,7 +42,6 @@ class JBrowseCommand extends core_1.Command {
         }
         return result;
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
     async writeJsonFile(location, contents) {
         this.debug(`Writing JSON file to ${process.cwd()} ${location}`);
         return fs_1.promises.writeFile(location, JSON.stringify(contents, null, 2));
@@ -105,11 +104,11 @@ class JBrowseCommand extends core_1.Command {
     }
     async getLatest() {
         for await (const versions of this.fetchVersions()) {
-            // if a release was just uploaded, or an erroneous build was made
-            // then it might have no build asset
+            // if a release was just uploaded, or an erroneous build was made then it
+            // might have no build asset
             const nonprereleases = versions
-                .filter(release => release.prerelease === false)
-                .filter(release => release.assets && release.assets.length > 0);
+                .filter(release => !release.prerelease)
+                .filter(release => release.assets?.length);
             if (nonprereleases.length > 0) {
                 // @ts-expect-error
                 const file = nonprereleases[0].assets.find(f => f.name.includes('jbrowse-web'))?.browser_download_url;
@@ -125,22 +124,23 @@ class JBrowseCommand extends core_1.Command {
         let page = 1;
         let result;
         do {
-            const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`);
+            const url = `https://api.github.com/repos/GMOD/jbrowse-components/releases?page=${page}`;
+            const response = await (0, fetchWithProxy_1.default)(url);
             if (response.ok) {
                 result = (await response.json());
                 yield result.filter(release => release.tag_name.startsWith('v'));
                 page++;
             }
             else {
-                throw new Error(`${response.statusText}`);
+                throw new Error(`HTTP ${response.status} fetching ${url}`);
             }
-        } while (result && result.length > 0);
+        } while (result.length);
     }
     async getTag(tag) {
         const response = await (0, fetchWithProxy_1.default)(`https://api.github.com/repos/GMOD/jbrowse-components/releases/tags/${tag}`);
         if (response.ok) {
             const result = (await response.json());
-            const file = result?.assets?.find(f => f.name.includes('jbrowse-web'))?.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

@@ -23,10 +23,10 @@ class AddAssembly extends base_1.default {
         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 });
+            this.error('Please specify the loading operation for this file with --load copy|symlink|move|inPlace', { exit: 110 });
         }
         else if (!this.needLoadData(argsSequence) && runFlags.load) {
-            this.error(`URL detected with --load flag. Please rerun the function without the --load flag`, { exit: 120 });
+            this.error('URL detected with --load flag. Please rerun the function without the --load flag', { exit: 120 });
         }
         let { name } = runFlags;
         let { type } = runFlags;
@@ -192,7 +192,11 @@ 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 exists = (s) => new Promise(r => {
+            fs_1.default.access(s, fs_1.default.constants.F_OK, e => {
+                r(!e);
+            });
+        });
         const { args: runArgs, flags: runFlags } = await this.parse(AddAssembly);
         const output = runFlags.target || runFlags.out || '.';
         if (!(await exists(output))) {

package/lib/commands/add-connection.js

@@ -82,26 +82,19 @@ class AddConnection extends base_1.default {
         catch (error) {
             this.error('The location provided is not a valid URL', { exit: 160 });
         }
-        if (locationUrl) {
-            let response;
-            try {
-                if (check) {
-                    // @ts-expect-error
-                    response = await (0, fetchWithProxy_1.default)(locationUrl, { method: 'HEAD' });
-                }
-                if (!response || response.ok) {
-                    return locationUrl.href;
+        try {
+            if (check) {
+                const response = await (0, fetchWithProxy_1.default)(`${locationUrl}`, { method: 'HEAD' });
+                if (!response.ok) {
+                    this.error(`Response returned with code ${response.status}`);
                 }
-                this.error(`Response returned with code ${response.status}`);
-            }
-            catch (error) {
-                // ignore
-                this.error(`Unable to fetch from URL, ${error}`, { exit: 170 });
             }
+            return locationUrl.href;
+        }
+        catch (error) {
+            // ignore
+            this.error(`Unable to fetch from URL, ${error}`, { exit: 170 });
         }
-        return this.error(`Could not resolve to a URL: "${location}"`, {
-            exit: 180,
-        });
     }
     determineConnectionType(url) {
         if (path_1.default.basename(url) === 'hub.txt') {
@@ -134,7 +127,7 @@ AddConnection.examples = [
 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/ `,
+        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 = {

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

@@ -23,7 +23,7 @@ class AddTrackJson extends base_1.default {
         }
         const idx = config.tracks.findIndex(({ trackId }) => trackId === track.trackId);
         if (idx !== -1) {
-            const existing = config.tracks[idx].name;
+            const existing = config.tracks[idx]?.name;
             this.debug(`Found existing track ${existing} in configuration`);
             if (update) {
                 this.debug(`Overwriting track ${existing} in configuration`);
@@ -49,13 +49,13 @@ AddTrackJson.examples = [
 AddTrackJson.args = {
     track: core_1.Args.string({
         required: true,
-        description: `track JSON file or command line arg blob`,
+        description: 'track JSON file or command line arg blob',
     }),
 };
 AddTrackJson.flags = {
     update: core_1.Flags.boolean({
         char: 'u',
-        description: `update the contents of an existing track, matched based on trackId`,
+        description: 'update the contents of an existing track, matched based on trackId',
     }),
     target: core_1.Flags.string({
         description: 'path to config file in JB2 installation directory to write out to.\nCreates ./config.json if nonexistent',

package/lib/commands/add-track.js

@@ -129,7 +129,7 @@ class AddTrack extends base_1.default {
         trackType = trackType || this.guessTrackType(adapter.type);
         trackId = trackId || path_1.default.basename(location, path_1.default.extname(location));
         name = name || trackId;
-        assemblyNames = assemblyNames || configContents.assemblies[0].name;
+        assemblyNames = assemblyNames || configContents.assemblies[0]?.name || '';
         const configObj = config ? (0, json_parse_better_errors_1.default)(config) : {};
         const trackConfig = {
             type: trackType,
@@ -145,6 +145,7 @@ class AddTrack extends base_1.default {
         if (trackType === 'AlignmentsTrack') {
             const assembly = configContents.assemblies.find(asm => asm.name === assemblyNames);
             if (assembly) {
+                // @ts-expect-error
                 trackConfig.adapter.sequenceAdapter = assembly.sequence.adapter;
             }
             else if (!skipCheck) {
@@ -445,27 +446,7 @@ class AddTrack extends base_1.default {
         };
     }
     guessTrackType(adapterType) {
-        const known = {
-            BamAdapter: 'AlignmentsTrack',
-            CramAdapter: 'AlignmentsTrack',
-            BgzipFastaAdapter: 'ReferenceSequenceTrack',
-            BigWigAdapter: 'QuantitativeTrack',
-            IndexedFastaAdapter: 'ReferenceSequenceTrack',
-            TwoBitAdapter: 'ReferenceSequenceTrack',
-            VcfTabixAdapter: 'VariantTrack',
-            VcfAdapter: 'VariantTrack',
-            BedpeAdapter: 'VariantTrack',
-            BedAdapter: 'FeatureTrack',
-            HicAdapter: 'HicTrack',
-            PAFAdapter: 'SyntenyTrack',
-            DeltaAdapter: 'SyntenyTrack',
-            ChainAdapter: 'SyntenyTrack',
-            MashMapAdapter: 'SyntenyTrack',
-            PairwiseIndexedPAFAdapter: 'SyntenyTrack',
-            MCScanAnchorsAdapter: 'SyntenyTrack',
-            MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
-        };
-        return known[adapterType] || 'FeatureTrack';
+        return adapterTypesToTrackTypeMap[adapterType] || 'FeatureTrack';
     }
 }
 AddTrack.description = 'Add a track to a JBrowse 2 configuration';
@@ -476,7 +457,7 @@ AddTrack.examples = [
     '# 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`,
+    '# 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',
@@ -491,13 +472,13 @@ AddTrack.examples = [
 AddTrack.args = {
     track: core_1.Args.string({
         required: true,
-        description: `Track file or URL`,
+        description: 'Track file or URL',
     }),
 };
 AddTrack.flags = {
     trackType: core_1.Flags.string({
         char: 't',
-        description: `Type of track, by default inferred from track file`,
+        description: 'Type of track, by default inferred from track file',
     }),
     name: core_1.Flags.string({
         char: 'n',
@@ -561,3 +542,23 @@ AddTrack.flags = {
     }),
 };
 exports.default = AddTrack;
+const adapterTypesToTrackTypeMap = {
+    BamAdapter: 'AlignmentsTrack',
+    CramAdapter: 'AlignmentsTrack',
+    BgzipFastaAdapter: 'ReferenceSequenceTrack',
+    BigWigAdapter: 'QuantitativeTrack',
+    IndexedFastaAdapter: 'ReferenceSequenceTrack',
+    TwoBitAdapter: 'ReferenceSequenceTrack',
+    VcfTabixAdapter: 'VariantTrack',
+    VcfAdapter: 'VariantTrack',
+    BedpeAdapter: 'VariantTrack',
+    BedAdapter: 'FeatureTrack',
+    HicAdapter: 'HicTrack',
+    PAFAdapter: 'SyntenyTrack',
+    DeltaAdapter: 'SyntenyTrack',
+    ChainAdapter: 'SyntenyTrack',
+    MashMapAdapter: 'SyntenyTrack',
+    PairwiseIndexedPAFAdapter: 'SyntenyTrack',
+    MCScanAnchorsAdapter: 'SyntenyTrack',
+    MCScanSimpleAnchorsAdapter: 'SyntenyTrack',
+};

package/lib/commands/admin-server.js

@@ -46,11 +46,11 @@ class AdminServer extends base_1.default {
         // start server with admin key in URL query string
         let port = 9090;
         if (runFlags.port) {
-            if (!isValidPort(parseInt(runFlags.port, 10))) {
+            if (!isValidPort(Number.parseInt(runFlags.port, 10))) {
                 this.error(`${runFlags.port} is not a valid port`);
             }
             else {
-                port = parseInt(runFlags.port, 10);
+                port = Number.parseInt(runFlags.port, 10);
             }
         }
         const app = (0, express_1.default)();

package/lib/commands/create.js

@@ -79,7 +79,7 @@ Create.examples = [
 Create.args = {
     localPath: core_1.Args.string({
         required: true,
-        description: `Location where JBrowse 2 will be installed`,
+        description: 'Location where JBrowse 2 will be installed',
     }),
 };
 Create.flags = {

package/lib/commands/make-pif.js

@@ -18,7 +18,7 @@ const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 function getReadline(filename) {
     const stream = fs_1.default.createReadStream(filename);
     return readline_1.default.createInterface({
-        input: filename.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+        input: /.b?gz$/.exec(filename) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
     });
 }
 function getStdReadline() {
@@ -53,7 +53,7 @@ async function createPIF(filename, stream) {
     const rl1 = filename ? getReadline(filename) : getStdReadline();
     for await (const line of rl1) {
         const [c1, l1, s1, e1, strand, c2, l2, s2, e2, ...rest] = line.split('\t');
-        stream.write([`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t') + '\n');
+        stream.write(`${[`t${c2}`, l2, s2, e2, strand, c1, l1, s1, e1, ...rest].join('\t')}\n`);
         const cigarIdx = rest.findIndex(f => f.startsWith('cg:Z'));
         const CIGAR = rest[cigarIdx];
         if (CIGAR) {
@@ -61,7 +61,7 @@ async function createPIF(filename, stream) {
                 ? flipCigar(parseCigar(CIGAR.slice(5))).join('')
                 : swapIndelCigar(CIGAR.slice(5))}`;
         }
-        stream.write([`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t') + '\n');
+        stream.write(`${[`q${c1}`, l1, s1, e1, strand, c2, l2, s2, e2, ...rest].join('\t')}\n`);
     }
     rl1.close();
 }
@@ -110,7 +110,7 @@ MakePIF.flags = {
 MakePIF.args = {
     file: core_1.Args.string({
         required: true,
-        description: `PAF file as input`,
+        description: 'PAF file as input',
     }),
 };
 exports.default = MakePIF;

package/lib/commands/remove-track.js

@@ -23,7 +23,7 @@ RemoveTrackJson.examples = ['$ jbrowse remove-track-json trackId'];
 RemoveTrackJson.args = {
     track: core_1.Args.string({
         required: true,
-        description: `track JSON file or command line arg blob`,
+        description: 'track JSON file or command line arg blob',
     }),
 };
 RemoveTrackJson.flags = {

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

@@ -17,7 +17,7 @@ class SetDefaultSession extends base_1.default {
         this.target = isDir ? `${output}/config.json` : output;
         const configContents = await this.readJsonFile(this.target);
         if (deleteDefaultSession) {
-            delete configContents.defaultSession;
+            configContents.defaultSession = undefined;
             await this.writeJsonFile(this.target, configContents);
         }
         else if (currentSession) {
@@ -25,7 +25,7 @@ class SetDefaultSession extends base_1.default {
             this.exit();
         }
         else if (!session) {
-            this.error(`Please provide a --session file`, { exit: 120 });
+            this.error('Please provide a --session file', { exit: 120 });
         }
         else if (session) {
             await this.writeJsonFile(this.target, {

package/lib/commands/sort-gff.js

@@ -36,7 +36,7 @@ SortGff.examples = [
 SortGff.args = {
     file: core_1.Args.string({
         required: true,
-        description: `GFF file`,
+        description: 'GFF file',
     }),
 };
 SortGff.flags = {

package/lib/commands/text-index.js

@@ -53,21 +53,21 @@ class TextIndex extends base_1.default {
         const asms = assemblies?.split(',') ||
             config.assemblies?.map(a => a.name) ||
             (config.assembly ? [config.assembly.name] : []);
-        if (!asms?.length) {
+        if (!asms.length) {
             throw new Error('No assemblies found');
         }
         for (const asm of asms) {
             const trackConfigs = await this.getTrackConfigs(confPath, tracks?.split(','), asm);
             if (!trackConfigs.length) {
-                this.log('Indexing assembly ' + asm + '...(no tracks found)...');
+                this.log(`Indexing assembly ${asm}...(no tracks found)...`);
                 continue;
             }
-            this.log('Indexing assembly ' + asm + '...');
+            this.log(`Indexing assembly ${asm}...`);
             if (dryrun) {
-                this.log(trackConfigs.map(e => `${e.trackId}\t${e.adapter.type}`).join('\n'));
+                this.log(trackConfigs.map(e => `${e.trackId}\t${e.adapter?.type}`).join('\n'));
             }
             else {
-                const id = asm + '-index';
+                const id = `${asm}-index`;
                 const idx = aggregateTextSearchAdapters.findIndex(x => x.textSearchAdapterId === id);
                 if (idx !== -1 && !force) {
                     this.log(`Note: ${asm} has already been indexed with this configuration, use --force to overwrite this assembly. Skipping for now`);
@@ -133,7 +133,7 @@ class TextIndex extends base_1.default {
         }
         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.`);
+            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;
@@ -141,7 +141,7 @@ class TextIndex extends base_1.default {
                 this.log(`Note: ${trackId} has already been indexed with this configuration, use --force to overwrite this track. Skipping for now`);
                 continue;
             }
-            this.log('Indexing track ' + trackId + '...');
+            this.log(`Indexing track ${trackId}...`);
             await this.indexDriver({
                 trackConfigs: [trackConfig],
                 attributes: attributes.split(','),
@@ -162,7 +162,7 @@ class TextIndex extends base_1.default {
                             ...textSearching,
                             textSearchAdapter: {
                                 type: 'TrixTextSearchAdapter',
-                                textSearchAdapterId: trackId + '-index',
+                                textSearchAdapterId: `${trackId}-index`,
                                 ixFilePath: {
                                     uri: `trix/${trackId}.ix`,
                                     locationType: 'UriLocation',
@@ -200,7 +200,7 @@ 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));
+            .filter(fileConfig => (0, common_1.supported)(fileConfig.adapter?.type));
         if (fileId?.length) {
             for (let i = 0; i < fileId.length; i++) {
                 trackConfigs[i].trackId = fileId[i];
@@ -226,7 +226,7 @@ class TextIndex extends base_1.default {
             quiet,
             typesToExclude,
         }));
-        const ixIxxStream = await this.runIxIxx({
+        await this.runIxIxx({
             readStream,
             outLocation,
             name,
@@ -240,27 +240,30 @@ class TextIndex extends base_1.default {
             typesToExclude,
             assemblyNames,
         });
-        return ixIxxStream;
     }
     async *indexFiles({ trackConfigs, attributes, outLocation, quiet, typesToExclude, }) {
         for (const config of trackConfigs) {
             const { adapter, textSearching } = config;
-            const { type } = adapter;
+            const { type } = adapter || {};
             const { indexingFeatureTypesToExclude = typesToExclude, indexingAttributes = attributes, } = textSearching || {};
             let loc;
             if (type === 'Gff3TabixAdapter') {
+                // @ts-expect-error
                 loc = adapter.gffGzLocation;
             }
             else if (type === 'Gff3Adapter') {
+                // @ts-expect-error
                 loc = adapter.gffLocation;
             }
             else if (type === 'VcfAdapter') {
+                // @ts-expect-error
                 loc = adapter.vcfLocation;
             }
             else if (type === 'VcfTabixAdapter') {
+                // @ts-expect-error
                 loc = adapter.vcfGzLocation;
             }
-            if (!loc) {
+            else {
                 return;
             }
             if (type === 'Gff3TabixAdapter' || type === 'Gff3Adapter') {
@@ -273,6 +276,7 @@ class TextIndex extends base_1.default {
                     quiet,
                 });
             }
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             else if (type === 'VcfTabixAdapter' || type === 'VcfAdapter') {
                 yield* (0, vcfAdapter_1.indexVcf)({
                     config,
@@ -285,15 +289,15 @@ class TextIndex extends base_1.default {
             }
         }
     }
-    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', `${name}.ixx`), prefixSize);
+    async runIxIxx({ readStream, outLocation, name, prefixSize, }) {
+        await (0, ixixx_1.ixIxxStream)(readStream, path_1.default.join(outLocation, 'trix', `${name}.ix`), path_1.default.join(outLocation, 'trix', `${name}.ixx`), prefixSize);
     }
     async getTrackConfigs(configPath, trackIds, assemblyName) {
         const { tracks } = readConf(configPath);
         if (!tracks) {
             return [];
         }
-        const trackIdsToIndex = trackIds || 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);
@@ -326,7 +330,7 @@ TextIndex.examples = [
 TextIndex.flags = {
     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`,
+        description: 'Specific tracks to index, formatted as comma separated trackIds. If unspecified, indexes all available tracks',
     }),
     target: core_1.Flags.string({
         description: 'Path to config file in JB2 installation directory to read from.',

package/lib/commands/upgrade.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const core_1 = require("@oclif/core");
-const rimraf_1 = require("rimraf");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const decompress_1 = __importDefault(require("decompress"));
@@ -22,7 +21,7 @@ class Upgrade extends base_1.default {
         }
         this.debug(`Want to upgrade at: ${argsPath}`);
         if (!argsPath) {
-            this.error(`No directory supplied`, { exit: 100 });
+            this.error('No directory supplied', { exit: 100 });
         }
         if (!fs_1.default.existsSync(path_1.default.join(argsPath, 'manifest.json'))) {
             this.error(`No manifest.json found in this directory, are you sure it is an
@@ -44,10 +43,12 @@ class Upgrade extends base_1.default {
             this.error('The URL provided does not seem to be a JBrowse installation URL');
         }
         if (clean) {
-            (0, rimraf_1.rimrafSync)(path_1.default.join(argsPath, 'static'));
+            fs_1.default.rmSync(path_1.default.join(argsPath, 'static'), { recursive: true, force: true });
             fs_1.default.readdirSync(argsPath)
                 .filter(f => f.includes('worker.js'))
-                .forEach(f => fs_1.default.unlinkSync(path_1.default.join(argsPath, f)));
+                .forEach(f => {
+                fs_1.default.unlinkSync(path_1.default.join(argsPath, f));
+            });
         }
         await (0, decompress_1.default)(Buffer.from(await response.arrayBuffer()), argsPath);
         this.log(`Unpacked ${locationUrl} at ${argsPath}`);
@@ -76,7 +77,7 @@ Upgrade.examples = [
 Upgrade.args = {
     localPath: core_1.Args.string({
         required: false,
-        description: `Location where JBrowse 2 is installed`,
+        description: 'Location where JBrowse 2 is installed',
         default: '.',
     }),
 };

package/lib/types/common.js

@@ -12,11 +12,11 @@ const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const fetchWithProxy_1 = __importDefault(require("../fetchWithProxy"));
 async function createRemoteStream(urlIn) {
-    const response = await (0, fetchWithProxy_1.default)(urlIn);
-    if (!response.ok) {
-        throw new Error(`Failed to fetch ${urlIn} status ${response.status} ${await response.text()}`);
+    const res = await (0, fetchWithProxy_1.default)(urlIn);
+    if (!res.ok) {
+        throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
     }
-    return response;
+    return res;
 }
 function isURL(FileName) {
     let url;
@@ -44,7 +44,6 @@ function makeLocation(location, protocol) {
     throw new Error(`invalid protocol ${protocol}`);
 }
 function guessAdapterFromFileName(filePath) {
-    // const uri = isURL(filePath) ? filePath : path.resolve(filePath)
     const protocol = isURL(filePath) ? 'uri' : 'localPath';
     const name = path_1.default.basename(filePath);
     if (/\.vcf\.b?gz$/i.test(filePath)) {
@@ -106,7 +105,7 @@ function guessAdapterFromFileName(filePath) {
         throw new Error(`Unsupported file type ${filePath}`);
     }
 }
-function supported(type) {
+function supported(type = '') {
     return [
         'Gff3TabixAdapter',
         'VcfTabixAdapter',

package/lib/types/gff3Adapter.js

@@ -13,7 +13,7 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
     // progress bar code was aided by blog post at
     // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
     const progressBar = new cli_progress_1.SingleBar({
-        format: '{bar} ' + trackId + ' {percentage}% | ETA: {eta}s',
+        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
         etaBuffer: 2000,
     }, cli_progress_1.Presets.shades_classic);
     let receivedBytes = 0;
@@ -28,7 +28,7 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
     });
     const rl = readline_1.default.createInterface({
         // @ts-expect-error
-        input: inLocation.match(/.b?gz$/) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
+        input: /.b?gz$/.exec(inLocation) ? stream.pipe((0, zlib_1.createGunzip)()) : stream,
     });
     for await (const line of rl) {
         if (!line.trim()) {
@@ -52,7 +52,9 @@ async function* indexGff3({ config, attributesToIndex, inLocation, outLocation,
                 .map(f => f.split('='))
                 .map(([key, val]) => [
                 key.trim(),
-                (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' '),
+                val
+                    ? (0, util_1.decodeURIComponentNoThrow)(val).trim().split(',').join(' ')
+                    : undefined,
             ]));
             const attrs = attributesToIndex
                 .map(attr => col9attrs[attr])

package/lib/types/vcfAdapter.js

@@ -13,7 +13,7 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
     // progress bar code was aided by blog post at
     // https://webomnizz.com/download-a-file-with-progressbar-using-node-js/
     const progressBar = new cli_progress_1.SingleBar({
-        format: '{bar} ' + trackId + ' {percentage}% | ETA: {eta}s',
+        format: `{bar} ${trackId} {percentage}% | ETA: {eta}s`,
         etaBuffer: 2000,
     }, cli_progress_1.Presets.shades_classic);
     let receivedBytes = 0;
@@ -26,7 +26,7 @@ async function* indexVcf({ config, attributesToIndex, inLocation, outLocation, q
         receivedBytes += chunk.length;
         progressBar.update(receivedBytes);
     });
-    const gzStream = inLocation.match(/.b?gz$/)
+    const gzStream = /.b?gz$/.exec(inLocation)
         ? // @ts-expect-error
             stream.pipe((0, zlib_1.createGunzip)())
         : stream;

package/lib/util.js

@@ -9,19 +9,20 @@ const common_1 = require("./types/common");
 const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 async function getLocalOrRemoteStream(uri, out) {
-    let stream;
-    let totalBytes = 0;
     if ((0, common_1.isURL)(uri)) {
         const result = await (0, common_1.createRemoteStream)(uri);
-        totalBytes = +(result.headers.get('Content-Length') || 0);
-        stream = result.body;
+        return {
+            totalBytes: +(result.headers.get('Content-Length') || 0),
+            stream: result.body,
+        };
     }
     else {
         const filename = path_1.default.isAbsolute(uri) ? uri : path_1.default.join(out, uri);
-        totalBytes = fs_1.default.statSync(filename).size;
-        stream = fs_1.default.createReadStream(filename);
+        return {
+            totalBytes: fs_1.default.statSync(filename).size,
+            stream: fs_1.default.createReadStream(filename),
+        };
     }
-    return { totalBytes, stream };
 }
 function decodeURIComponentNoThrow(uri) {
     try {

package/oclif.manifest.json

@@ -1127,5 +1127,5 @@
       ]
     }
   },
-  "version": "2.13.1"
+  "version": "2.14.0"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "2.13.1",
+  "version": "2.14.0",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -57,7 +57,6 @@
     "ixixx": "^2.0.1",
     "json-parse-better-errors": "^1.0.2",
     "node-fetch-native": "^1.6.4",
-    "rimraf": "^5.0.0",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
@@ -74,5 +73,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "fcebca71cc1d066654603e1a9accfa6c6d4f764d"
+  "gitHead": "9fb8231d932db40adf0a283081765431756c66ff"
 }