From efc27186d4afd931a6b1d91772cadecc8d4169b1 Mon Sep 17 00:00:00 2001
From: jplfaria <jplfaria@gmail.com>
Date: Tue, 16 Jun 2026 20:43:41 +0000
Subject: [PATCH 1/2] fix(reconstruct): ensure workspace folder exists before
 first write

---
 src/modelseed_api/jobs/tasks.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/modelseed_api/jobs/tasks.py b/src/modelseed_api/jobs/tasks.py
index 771191d..0e2edb1 100644
--- a/src/modelseed_api/jobs/tasks.py
+++ b/src/modelseed_api/jobs/tasks.py
@@ -72,6 +72,18 @@ def _merge_ws_metadata(ws, obj_path: str, new_meta: dict):
     ws.update_metadata({"objects": [[obj_path, merged]]})
 
 
+def _ensure_ws_folder(ws, path: str) -> None:
+    """Create workspace folder at path if it does not exist (idempotent).
+
+    PATRIC workspace returns Insufficient permissions instead of Not Found
+    when creating inside a missing intermediate directory. This is the root
+    cause for first-time users who have no /username/modelseed folder yet.
+    """
+    if not path or path.rstrip("/") in ("", "/"):
+        return
+    ws.create({"objects": [[path.rstrip("/"), "folder", {}, ""]], "overwrite": 1})
+
+
 def _load_template(template_type: str):
     """Load a template from local JSON file using MSTemplateBuilder."""
     from modelseedpy import MSTemplateBuilder
@@ -768,6 +780,7 @@ def reconstruct(
             "fba_count": "0",
         }
 
+        _ensure_ws_folder(ws, output_path.rsplit("/", 1)[0])
         ws.create({
             "objects": [
                 [output_path, "modelfolder", folder_meta, ""],
@@ -1342,6 +1355,8 @@ def _progress(msg: str) -> None:
     data_dir = str(kbann.annoontology_dir / "data")
 
     ws = get_storage_service(token)
+    _ensure_ws_folder(ws, output_path.rsplit("/", 1)[0])
+    _ensure_ws_folder(ws, output_path)
     _progress(f"Preparing batch of {len(genomes)} genome(s)...")
 
     all_rxn_rows: list = []

From 6c4edf4458ab1cdde7c26ab5910cdb45e5cdbefa Mon Sep 17 00:00:00 2001
From: jplfaria <jplfaria@gmail.com>
Date: Tue, 16 Jun 2026 20:44:48 +0000
Subject: [PATCH 2/2] test(tasks): add unit tests for _ensure_ws_folder helper

---
 tests/unit/test_ensure_ws_folder.py | 40 +++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 tests/unit/test_ensure_ws_folder.py

diff --git a/tests/unit/test_ensure_ws_folder.py b/tests/unit/test_ensure_ws_folder.py
new file mode 100644
index 0000000..f4fe1ca
--- /dev/null
+++ b/tests/unit/test_ensure_ws_folder.py
@@ -0,0 +1,40 @@
+"""Tests for _ensure_ws_folder.
+
+Regression for ModelSEED/modelseed-api-ops#11: PATRIC workspace returns
+"Insufficient permissions" instead of "Not Found" when creating inside
+a missing intermediate directory, which hits first-time users who have
+not yet had a /username/modelseed folder created.
+"""
+from unittest.mock import MagicMock
+
+from modelseed_api.jobs.tasks import _ensure_ws_folder
+
+
+def test_creates_folder():
+    ws = MagicMock()
+    _ensure_ws_folder(ws, "/alice/modelseed")
+    ws.create.assert_called_once_with(
+        {"objects": [["/alice/modelseed", "folder", {}, ""]], "overwrite": 1}
+    )
+
+
+def test_strips_trailing_slash():
+    ws = MagicMock()
+    _ensure_ws_folder(ws, "/alice/modelseed/")
+    ws.create.assert_called_once_with(
+        {"objects": [["/alice/modelseed", "folder", {}, ""]], "overwrite": 1}
+    )
+
+
+def test_noop_for_root_and_empty():
+    ws = MagicMock()
+    _ensure_ws_folder(ws, "")
+    _ensure_ws_folder(ws, "/")
+    _ensure_ws_folder(ws, "//")
+    ws.create.assert_not_called()
+
+
+def test_noop_for_none():
+    ws = MagicMock()
+    _ensure_ws_folder(ws, None)
+    ws.create.assert_not_called()