@jbrowse/cli 4.3.0 → 5.0.0-beta.10

package/dist/index.js

@@ -1,35 +1,90 @@
 #!/usr/bin/env node
-import { parseArgs } from 'util';
-// Command imports
-import { run as addAssemblyRun } from "./commands/add-assembly/index.js";
-import { run as addConnectionRun } from "./commands/add-connection.js";
-import { run as addTrackJsonRun } from "./commands/add-track-json.js";
-import { run as addTrackRun } from "./commands/add-track.js";
-import { run as adminServerRun } from "./commands/admin-server/index.js";
-import { run as createRun } from "./commands/create.js";
-import { run as makePIFRun } from "./commands/make-pif/index.js";
-import { run as removeTrackRun } from "./commands/remove-track.js";
-import { run as setDefaultSessionRun } from "./commands/set-default-session.js";
-import { run as sortBedRun } from "./commands/sort-bed.js";
-import { run as sortGffRun } from "./commands/sort-gff.js";
-import { run as textIndexRun } from "./commands/text-index/index.js";
-import { run as upgradeRun } from "./commands/upgrade.js";
-import { version } from "./version.js";
-const commands = {
-    create: createRun,
-    'add-assembly': addAssemblyRun,
-    'add-track': addTrackRun,
-    'text-index': textIndexRun,
-    'admin-server': adminServerRun,
-    upgrade: upgradeRun,
-    'make-pif': makePIFRun,
-    'sort-gff': sortGffRun,
-    'sort-bed': sortBedRun,
-    'add-connection': addConnectionRun,
-    'add-track-json': addTrackJsonRun,
-    'remove-track': removeTrackRun,
-    'set-default-session': setDefaultSessionRun,
-};
+import { parseArgs } from 'node:util';
+import { version } from './version.js';
+// single source of truth for both dispatch and the global help listing, so a
+// new command can never be wired into one but forgotten in the other.
+//
+// Each command is LOADED WHEN IT IS DISPATCHED, not imported here: a static
+// import list makes every invocation pay for every command's module graph, and
+// text-index's parsers alone are most of it. `jbrowse add-track` went from
+// 0.35s to 0.21s of startup, which is the whole of what that command does.
+const registry = [
+    {
+        name: 'create',
+        summary: 'Downloads and installs the latest JBrowse 2 release',
+        load: () => import('./commands/create.js').then(m => m.run),
+    },
+    {
+        name: 'add-assembly',
+        summary: 'Add an assembly to a JBrowse 2 configuration',
+        load: () => import('./commands/add-assembly/index.js').then(m => m.run),
+    },
+    {
+        name: 'add-track',
+        summary: 'Add a track to a JBrowse 2 configuration',
+        load: () => import('./commands/add-track.js').then(m => m.run),
+    },
+    {
+        name: 'validate',
+        summary: 'Check a configuration for errors, including ones JBrowse accepts silently',
+        load: () => import('./commands/validate/index.js').then(m => m.run),
+    },
+    {
+        name: 'text-index',
+        summary: 'Make a text-indexing file for any given track(s)',
+        load: () => import('./commands/text-index/index.js').then(m => m.run),
+    },
+    {
+        name: 'admin-server',
+        summary: 'Start up a small admin server for JBrowse configuration',
+        load: () => import('./commands/admin-server/index.js').then(m => m.run),
+    },
+    {
+        name: 'upgrade',
+        summary: 'Upgrades JBrowse 2 to latest version',
+        load: () => import('./commands/upgrade.js').then(m => m.run),
+    },
+    {
+        name: 'make-pif',
+        summary: 'Creates pairwise indexed PAF (PIF), with bgzip and tabix',
+        load: () => import('./commands/make-pif/index.js').then(m => m.run),
+    },
+    {
+        name: 'make-density',
+        summary: 'Counts feature starts per bin into a bigWig density sidecar, with bedGraphToBigWig',
+        load: () => import('./commands/make-density/index.js').then(m => m.run),
+    },
+    {
+        name: 'sort-gff',
+        summary: 'Sort a GFF/GTF for tabix: sort -k1,1 -k4,4n, header kept on top',
+        load: () => import('./commands/sort-gff.js').then(m => m.run),
+    },
+    {
+        name: 'sort-bed',
+        summary: 'Sort a BED for tabix: sort -k1,1 -k2,2n, header kept on top',
+        load: () => import('./commands/sort-bed.js').then(m => m.run),
+    },
+    {
+        name: 'add-connection',
+        summary: 'Add a connection to a JBrowse 2 configuration',
+        load: () => import('./commands/add-connection.js').then(m => m.run),
+    },
+    {
+        name: 'add-track-json',
+        summary: 'Add a track configuration directly from a JSON hunk',
+        load: () => import('./commands/add-track-json.js').then(m => m.run),
+    },
+    {
+        name: 'remove-track',
+        summary: 'Remove a track configuration from a JBrowse 2 configuration',
+        load: () => import('./commands/remove-track.js').then(m => m.run),
+    },
+    {
+        name: 'set-default-session',
+        summary: 'Set a default session with views and tracks',
+        load: () => import('./commands/set-default-session.js').then(m => m.run),
+    },
+];
 export async function main(args) {
     try {
         const { values: flags, positionals } = parseArgs({
@@ -64,16 +119,23 @@ export async function main(args) {
             showGlobalHelp();
             process.exit(1);
         }
-        const command = commands[commandName];
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        const command = registry.find(c => c.name === commandName);
         if (!command) {
             console.error(`Error: Unknown command "${commandName}"`);
-            console.error(`Available commands: ${Object.keys(commands).join(', ')}`);
+            console.error(`Available commands: ${registry.map(c => c.name).join(', ')}`);
             process.exit(1);
         }
-        // Pass the remaining arguments to the command
-        const commandArgs = args.slice(1); // Remove the command name from args
-        await command(commandArgs);
+        // Pass everything after the command token to the command. Slicing from the
+        // command's actual position (rather than a hardcoded index 0) keeps this
+        // correct when a global flag precedes the command, e.g. `jbrowse -v create`
+        const commandArgs = args.slice(args.indexOf(commandName) + 1);
+        // ...but that slice drops a help flag written before the command, so
+        // `jbrowse --help create` used to run create with no args and fail on the
+        // missing positional instead of printing its help
+        if (flags.help && !commandArgs.some(a => a === '--help' || a === '-h')) {
+            commandArgs.push('--help');
+        }
+        await (await command.load())(commandArgs);
     }
     catch (error) {
         const message = error instanceof Error ? error.message : String(error);
@@ -93,6 +155,10 @@ Try setting a custom TMPDIR with more available space:
     }
 }
 function showGlobalHelp() {
+    const width = Math.max(...registry.map(c => c.name.length)) + 2;
+    const commandLines = registry
+        .map(c => `  ${c.name.padEnd(width)}${c.summary}`)
+        .join('\n');
     console.log(`
 JBrowse CLI
 
@@ -100,19 +166,7 @@ USAGE
   $ jbrowse <command> [options]
 
 COMMANDS
-  create               Downloads and installs the latest JBrowse 2 release
-  add-assembly         Add an assembly to a JBrowse 2 configuration
-  add-track            Add a track to a JBrowse 2 configuration
-  text-index           Make a text-indexing file for any given track(s)
-  admin-server         Start up a small admin server for JBrowse configuration
-  upgrade              Upgrades JBrowse 2 to latest version
-  make-pif             Creates pairwise indexed PAF (PIF), with bgzip and tabix
-  sort-gff             Helper utility to sort GFF files for tabix
-  sort-bed             Helper utility to sort BED files for tabix
-  add-connection       Add a connection to a JBrowse 2 configuration
-  add-track-json       Add a track configuration directly from a JSON hunk
-  remove-track         Remove a track configuration from a JBrowse 2 configuration
-  set-default-session  Set a default session with views and tracks
+${commandLines}
 
 OPTIONS
   -h, --help     Show help

package/dist/types/common.js

@@ -1,27 +1,3 @@
-import fetch from "../cliFetch.js";
-export async function createRemoteStream(urlIn) {
-    const res = await fetch(urlIn);
-    if (!res.ok) {
-        throw new Error(`Failed to fetch ${urlIn} status ${res.status} ${await res.text()}`);
-    }
-    return res;
-}
-export function isURL(FileName) {
-    let url;
-    try {
-        url = new URL(FileName);
-    }
-    catch (_) {
-        return false;
-    }
-    return url.protocol === 'http:' || url.protocol === 'https:';
-}
-const SUPPORTED_ADAPTERS = new Set([
-    'Gff3TabixAdapter',
-    'VcfTabixAdapter',
-    'Gff3Adapter',
-    'VcfAdapter',
-]);
-export function supported(type = '') {
-    return SUPPORTED_ADAPTERS.has(type);
-}
+// the indexer package owns both of these: which adapter types text-index can
+// handle, and the URL test its stream opener uses to pick fetch vs fs
+export { isURL, isSupportedIndexingAdapter as supported, } from '@jbrowse/text-indexing-core';