From 5518f9e4e610e1780cf992840aa801f9b551dfe4 Mon Sep 17 00:00:00 2001
From: Ryan Ratcliff <ryan.ratcliff@fountainlife.com>
Date: Tue, 10 Mar 2026 10:43:58 -0400
Subject: [PATCH] fix: use full path as prefix for recursive files download

Made-with: Cursor
---
 lib/cmds/files_cmds/download.js |  4 +++-
 test/unit/commands/file.test.js | 25 +++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/lib/cmds/files_cmds/download.js b/lib/cmds/files_cmds/download.js
index b49c713..5757d43 100644
--- a/lib/cmds/files_cmds/download.js
+++ b/lib/cmds/files_cmds/download.js
@@ -34,7 +34,9 @@ exports.builder = yargs => {
 
 exports.handler = async argv => {
   if (argv.recursive) {
-    const [datasetId, prefix] = argv.source.split('/');
+    const parts = argv.source.split('/').filter(Boolean);
+    const datasetId = parts[0];
+    const prefix = parts.length > 1 ? parts.slice(1).join('/') : '';
 
     const opts = {
       datasetId,
diff --git a/test/unit/commands/file.test.js b/test/unit/commands/file.test.js
index 4ff5d94..4c58219 100644
--- a/test/unit/commands/file.test.js
+++ b/test/unit/commands/file.test.js
@@ -250,6 +250,31 @@ test.serial.cb('The "files-download" command should download a set of files from
     .parse('download projectId/prefix /dir -r');
 });
 
+test.serial.cb('The "files-download" command should use full path as prefix for recursive download', t => {
+  listStub.onFirstCall().returns({
+    data: {
+      items: [
+        {
+          id: '1',
+          name: 'genomic-archive/snp-array-vcf-Build38/sample.vcf.gz'
+        }
+      ]
+    }
+  });
+
+  callback = () => {
+    t.is(listStub.callCount, 1);
+    t.is(listStub.getCall(0).args[1], '/v1/files?datasetId=projectId&pageSize=1000&name=genomic-archive%2Fsnp-array-vcf-Build38');
+    t.end();
+  };
+
+  t.context.deleteFileStub = t.context.sandbox.stub(fs, 'unlinkSync').callsFake(callback);
+  t.context.copyFileStub = t.context.sandbox.stub(fs, 'copyFileSync').callsFake(callback);
+
+  yargs.command(download)
+    .parse('download projectId/genomic-archive/snp-array-vcf-Build38/ . -r');
+});
+
 test.serial.cb('The "files-mv" command should move a set of files from a project', t => {
   patchStub.returns({});
   listStub.onFirstCall().returns({