@jbrowse/cli 5.0.0-beta.2 → 5.0.0-beta.4

package/README.md

@@ -264,9 +264,9 @@ Options:
   -a, --assemblyNames        Assembly name or names for track as comma separated
                              string. For pairwise synteny tracks the order is
                              query,target (reverse of minimap2/nucmer argument
-                             order); for all-vs-all adapters
-                             (AllVsAllPAFAdapter/AllVsAllIndexedPAFAdapter) list
-                             every assembly the file covers, in any order
+                             order); for the multi-genome PAF adapters
+                             (MultiGenomePAFAdapter/MultiGenomeIndexedPAFAdapter)
+                             list every assembly the file covers, in any order
 
       --category             Optional comma separated string of categories to
                              group tracks
@@ -352,10 +352,10 @@ Gff3TabixAdapter, GtfTabixAdapter, BedTabixAdapter, BigBedAdapter,
 VcfTabixAdapter and SplitVcfTabixAdapter.
 
 For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is query,target
-— the reverse of the minimap2/nucmer input order. For the all-vs-all adapters
-(AllVsAllPAFAdapter, AllVsAllIndexedPAFAdapter) it is instead the full list of
-assemblies the file covers, in any order, since one all-vs-all file backs every
-pair.
+— the reverse of the minimap2/nucmer input order. For the multi-genome PAF
+adapters (MultiGenomePAFAdapter, MultiGenomeIndexedPAFAdapter) it is instead the
+full list of assemblies the file covers, in any order, since one multi-genome
+file backs every pair.
 
 Examples:
 
@@ -564,6 +564,9 @@ Options:
   -p, --port                 Specified port to start the server on (default:
                              9090)
 
+      --host                 Interface to bind to (default: 127.0.0.1). Use
+                             0.0.0.0 to accept connections from other machines
+
       --root                 Path to the root of the JB2 installation
 
       --bodySizeLimit        Size limit of the update message (default: 25mb)
@@ -571,9 +574,10 @@ Options:
 Notes:
 
 The admin-server lets a browser session write changes back to config.json on
-disk, authorized by a one-time key printed in the startup URL. It is meant for
-local configuration only: run it on a trusted machine and do not expose the port
-to untrusted networks or the public internet.
+disk, authorized by a one-time key printed in the startup URL. It binds to
+127.0.0.1 so only this machine can reach it. The key gates the config routes,
+but the rest of the JBrowse directory is served unauthenticated, so widen --host
+only on a trusted network.
 
 Examples:
 
@@ -588,6 +592,9 @@ $ jbrowse admin-server --root /path/to/jb2/
 
 # raise the body size limit for very large config updates
 $ jbrowse admin-server --bodySizeLimit 100mb
+
+# accept connections from other machines on the network
+$ jbrowse admin-server --host 0.0.0.0
 ```
 
 

package/dist/commands/add-track.js

@@ -39,7 +39,7 @@ export async function run(args) {
         assemblyNames: {
             type: 'string',
             short: 'a',
-            description: 'Assembly name or names for track as comma separated string. For pairwise synteny tracks the order is query,target (reverse of minimap2/nucmer argument order); for all-vs-all adapters (AllVsAllPAFAdapter/AllVsAllIndexedPAFAdapter) list every assembly the file covers, in any order',
+            description: 'Assembly name or names for track as comma separated string. For pairwise synteny tracks the order is query,target (reverse of minimap2/nucmer argument order); for the multi-genome PAF adapters (MultiGenomePAFAdapter/MultiGenomeIndexedPAFAdapter) list every assembly the file covers, in any order',
         },
         category: {
             type: 'string',
@@ -147,9 +147,9 @@ export async function run(args) {
         'BigBedAdapter, VcfTabixAdapter and SplitVcfTabixAdapter.\n\n' +
         'For pairwise synteny adapters (PAF/Delta/Chain) --assemblyNames is ' +
         'query,target — the reverse of the minimap2/nucmer input order. For the ' +
-        'all-vs-all adapters (AllVsAllPAFAdapter, AllVsAllIndexedPAFAdapter) it is ' +
+        'multi-genome PAF adapters (MultiGenomePAFAdapter, MultiGenomeIndexedPAFAdapter) it is ' +
         'instead the full list of assemblies the file covers, in any order, since ' +
-        'one all-vs-all file backs every pair.';
+        'one multi-genome file backs every pair.';
     const examples = [
         '# 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',

package/dist/commands/admin-server/index.js

@@ -13,6 +13,11 @@ export async function run(args) {
             short: 'p',
             description: 'Specified port to start the server on (default: 9090)',
         },
+        host: {
+            type: 'string',
+            description: 'Interface to bind to (default: 127.0.0.1). Use 0.0.0.0 to accept ' +
+                'connections from other machines',
+        },
         root: {
             type: 'string',
             description: 'Path to the root of the JB2 installation',
@@ -40,12 +45,15 @@ export async function run(args) {
         '',
         '# raise the body size limit for very large config updates',
         '$ jbrowse admin-server --bodySizeLimit 100mb',
+        '',
+        '# accept connections from other machines on the network',
+        '$ jbrowse admin-server --host 0.0.0.0',
     ];
     const notes = 'The admin-server lets a browser session write changes back to ' +
         'config.json on disk, authorized by a one-time key printed in the ' +
-        'startup URL. It is meant for local configuration only: run it on a ' +
-        'trusted machine and do not expose the port to untrusted networks or the ' +
-        'public internet.';
+        'startup URL. It binds to 127.0.0.1 so only this machine can reach it. ' +
+        'The key gates the config routes, but the rest of the JBrowse directory ' +
+        'is served unauthenticated, so widen --host only on a trusted network.';
     if (flags.help) {
         printHelp({
             description,
@@ -56,7 +64,7 @@ export async function run(args) {
         });
         return;
     }
-    const { root, bodySizeLimit = '25mb' } = flags;
+    const { root, host, bodySizeLimit = '25mb' } = flags;
     const { outFile, baseDir } = await setupConfigFile({ root });
     const port = parsePort({ portStr: flags.port });
     // the key lives only in this process and in the startup URL printed below. It
@@ -71,5 +79,5 @@ export async function run(args) {
         serverRef,
         bodySizeLimit: parseByteLimit(bodySizeLimit),
     }));
-    startServer({ server, port, key, outFile, serverRef });
+    startServer({ server, port, host, key, outFile, serverRef });
 }

package/dist/commands/admin-server/utils.js

@@ -4,6 +4,9 @@ import path from 'node:path';
 import handler from 'serve-handler';
 import { debug, isRecord, resolveConfigPath, writeJsonFile, } from '../../utils.js';
 import { createDefaultConfig } from '../add-assembly/utils.js';
+// Loopback, so the unauthenticated static handler below does not serve the
+// data directory to every host on the network. `--host` opts out.
+export const DEFAULT_HOST = '127.0.0.1';
 export function parsePort({ portStr, defaultPort = 9090, }) {
     if (!portStr) {
         return defaultPort;
@@ -122,9 +125,8 @@ function sendText(res, status, body) {
     res.writeHead(status, { 'Content-Type': 'text/plain; charset=utf-8' });
     res.end(body);
 }
-// What `cors()` sent. The server binds to localhost for a browser tab on the
-// same machine to talk to, and the admin key is what authorizes a write — the
-// origin never was.
+// What `cors()` sent. The admin key is what authorizes a write; the origin
+// never was.
 function applyCorsHeaders(res) {
     res.setHeader('Access-Control-Allow-Origin', '*');
     res.setHeader('Access-Control-Allow-Methods', 'GET, HEAD, POST, OPTIONS');
@@ -278,9 +280,9 @@ export function createRequestHandler({ baseDir, outFile, key, serverRef, bodySiz
         }
     };
 }
-export function startServer({ server, port, key, outFile, serverRef, }) {
-    server.listen(port, () => {
-        console.log(`Admin server started on port ${port}\n\n` +
+export function startServer({ server, port, host = DEFAULT_HOST, key, outFile, serverRef, }) {
+    server.listen(port, host, () => {
+        console.log(`Admin server started on ${host}:${port}\n\n` +
             `To access the admin interface, open your browser to:\n` +
             `http://localhost:${port}?adminKey=${key}\n\n` +
             `Admin key: ${key}\n` +

package/dist/commands/make-pif/index.js

@@ -159,7 +159,7 @@ export async function run(args) {
     }
     const nextCommand = samples.size > 0
         ? 'Next, add it as an all-vs-all synteny track (PanSN names detected):\n' +
-            `  jbrowse add-track ${outputFile} --adapterType AllVsAllIndexedPAFAdapter -a ${[...samples].sort().join(',')} --load copy`
+            `  jbrowse add-track ${outputFile} --adapterType MultiGenomeIndexedPAFAdapter -a ${[...samples].sort().join(',')} --load copy`
         : 'Next, add it as a synteny track (set -a to your query,target assembly names):\n' +
             `  jbrowse add-track ${outputFile} -a query,target --load copy`;
     console.log(`Created ${outputFile} and ${indexFile}\n\n${nextCommand}`);

package/dist/commands/text-index/adapter-utils.js

@@ -12,10 +12,6 @@ export function createTrixAdapter(name, assemblyNames, idSuffix = 'index') {
             uri: uris.ixx,
             locationType: 'UriLocation',
         },
-        metaFilePath: {
-            uri: uris.meta,
-            locationType: 'UriLocation',
-        },
         assemblyNames,
     };
 }