@jbrowse/cli 4.3.0 → 5.0.0-beta.2

package/dist/base.js

@@ -1,4 +1 @@
-/**
- * By convention, exit codes in this base class are below 100
- */
 export {};

package/dist/bin.js

@@ -1,5 +1,6 @@
 #!/usr/bin/env node
-import { main } from "./index.js";
+import { main } from './index.js';
 main(process.argv.slice(2)).catch((e) => {
     console.error(e);
+    process.exitCode = 1;
 });

package/dist/cliFetch.js

@@ -1,3 +1,6 @@
+// Wrapper around fetch that allows tests to mock API calls. All modules in
+// jbrowse-cli must use this instead of the global fetch function. See
+// CLAUDE.md for details.
 export default function cliFetch(url, options = {}) {
     return fetch(url, options);
 }

package/dist/commands/add-assembly/index.js

@@ -1,6 +1,10 @@
-import { parseArgs } from 'util';
-import { addAssemblyToConfig, enhanceAssembly, getAssembly, loadOrCreateConfig, resolveTargetPath, saveConfigAndReport, } from "./utils.js";
-import { debug, printHelp } from "../../utils.js";
+import path from 'node:path';
+import { parseArgs } from 'node:util';
+import { debug, printHelp, requirePositional } from '../../utils.js';
+import { loadFiles } from '../add-track-utils/file-operations.js';
+import { validateLoadOption } from '../add-track-utils/validators.js';
+import { saveConfigAndReport } from '../shared/config-operations.js';
+import { addAssemblyToConfig, enhanceAssembly, getAssembly, loadOrCreateConfig, parseSequenceType, resolveTargetPath, } from './utils.js';
 export async function run(args) {
     const options = {
         type: {
@@ -40,7 +44,6 @@ export async function run(args) {
             type: 'string',
             description: 'Type of aliases defined by --refNameAliases; if "custom", --refNameAliases is either a JSON file location or inline JSON that defines a custom sequence adapter',
             choices: ['aliases', 'custom'],
-            dependsOn: ['refNameAliases'],
         },
         refNameColors: {
             type: 'string',
@@ -65,18 +68,14 @@ export async function run(args) {
             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',
             choices: ['copy', 'symlink', 'move', 'inPlace'],
         },
-        skipCheck: {
-            type: 'boolean',
-            description: "Don't check whether or not the sequence file or URL exists or if you are in a JBrowse directory",
-        },
-        overwrite: {
-            type: 'boolean',
-            description: 'Overwrite existing assembly if one with the same name exists',
-        },
         force: {
             type: 'boolean',
             short: 'f',
-            description: 'Equivalent to `--skipCheck --overwrite`',
+            description: 'Overwrite existing assembly and skip file existence checks',
+        },
+        config: {
+            type: 'string',
+            description: 'Any extra config settings to add to the assembly',
         },
     };
     const { positionals, values: runFlags } = parseArgs({
@@ -85,6 +84,13 @@ export async function run(args) {
         allowPositionals: true,
     });
     const description = 'Add an assembly to a JBrowse 2 configuration';
+    const usage = 'jbrowse add-assembly <sequence> [options]';
+    const notes = '--config takes inline JSON (not a file path) that is merged into the ' +
+        'generated assembly config, so you can set fields the dedicated flags do ' +
+        'not cover. A "sequence" object in it is merged into the generated ' +
+        'ReferenceSequenceTrack rather than replacing it, e.g. --config ' +
+        '\'{"sequence":{"formatAbout":{"hideUris":true}}}\' hides file URIs in the ' +
+        "assembly's About dialog.";
     const examples = [
         '# add assembly to installation in current directory. assumes .fai file also exists, and copies GRCh38.fa and GRCh38.fa.fai to current directory',
         '$ jbrowse add-assembly GRCh38.fa --load copy',
@@ -109,32 +115,53 @@ export async function run(args) {
         '',
         '# 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',
+        '',
+        '# hide file URIs in the assembly About dialog',
+        '$ jbrowse add-assembly GRCh38.fa --load copy --config \'{"sequence":{"formatAbout":{"hideUris":true}}}\'',
     ];
     if (runFlags.help) {
         printHelp({
             description,
             examples,
-            usage: 'jbrowse add-assembly <sequence> [options]',
+            notes,
+            usage,
             options,
         });
         return;
     }
-    const argsSequence = positionals[0] || '';
+    validateLoadOption(runFlags.load);
+    const type = parseSequenceType(runFlags.type);
+    const argsSequence = positionals[0];
+    requirePositional(argsSequence, 'sequence', usage);
     const output = runFlags.target || runFlags.out || '.';
+    const flags = { ...runFlags, type };
     debug(`Sequence location is: ${argsSequence}`);
     const target = await resolveTargetPath(output);
-    const baseAssembly = await getAssembly({ runFlags, argsSequence, target });
-    const assembly = await enhanceAssembly(baseAssembly, runFlags);
+    const { assembly: baseAssembly, filesToLoad: sequenceFiles } = await getAssembly({
+        runFlags: flags,
+        argsSequence,
+    });
+    const { assembly, filesToLoad: aliasFiles } = await enhanceAssembly(baseAssembly, flags);
     const configContents = await loadOrCreateConfig(target);
     const { config: updatedConfig, wasOverwritten } = await addAssemblyToConfig({
         config: configContents,
         assembly,
-        runFlags,
+        runFlags: flags,
+    });
+    await loadFiles({
+        files: [...sequenceFiles, ...aliasFiles],
+        destDir: path.dirname(target),
+        mode: flags.load,
+        force: flags.force,
     });
     await saveConfigAndReport({
         config: updatedConfig,
         target,
-        assembly,
+        itemType: 'assembly',
+        itemName: assembly.name,
+        itemId: assembly.name,
         wasOverwritten,
     });
+    console.log(`\nNext, add tracks to this assembly (replace with your data file):\n` +
+        `  jbrowse add-track myfile.bam -a ${assembly.name} --load copy`);
 }