From ac07a7820bbe941d13b2cac2307e013ccf45191e Mon Sep 17 00:00:00 2001
From: Jas Kalayan <jkalayan@gmail.com>
Date: Fri, 3 Jul 2026 15:17:03 +0100
Subject: [PATCH] use UPLOAD_FOLDER as root dir for all uploaded files

---
 biosimdb_interface/form/extract.py |  8 ++++++--
 biosimdb_interface/form/upload.py  |  7 +++----
 biosimdb_interface/form/utils.py   | 10 ++++++++++
 3 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/biosimdb_interface/form/extract.py b/biosimdb_interface/form/extract.py
index eeddc64..244bce5 100644
--- a/biosimdb_interface/form/extract.py
+++ b/biosimdb_interface/form/extract.py
@@ -8,12 +8,13 @@
 """
 
 import os
-import tempfile
+import shutil
 
 from biosim_extractor.metadata.populatemetadata import MetadataPopulator
 from flask import jsonify, request, session
 
 from . import form_bp
+from .utils import make_upload_tmpdir
 
 
 def extract_files_validate(top_file, traj_file):
@@ -71,7 +72,8 @@ def extract_metadata():
         if not topology or not trajectories:
             return jsonify({"error": "Simulation files are missing."}), 400
 
-        with tempfile.TemporaryDirectory() as temp_dir:
+        temp_dir = make_upload_tmpdir("biosimdb_extract_")
+        try:
             topo_path = os.path.join(temp_dir, topology.filename)
             topology.save(topo_path)
             traj_files = []
@@ -100,6 +102,8 @@ def extract_metadata():
                         "message": "Metadata extracted successfully.",
                     }
                 )
+        finally:
+            shutil.rmtree(temp_dir, ignore_errors=True)
 
     except Exception as e:
         print(f"ERROR: {e}")
diff --git a/biosimdb_interface/form/upload.py b/biosimdb_interface/form/upload.py
index 7a73cbf..ba82290 100644
--- a/biosimdb_interface/form/upload.py
+++ b/biosimdb_interface/form/upload.py
@@ -4,14 +4,13 @@
 import json
 import os
 import shutil
-import tempfile
 
 from biosim_extractor.metadata.filemetadata import files_metadata
 from flask import current_app, request, session
 from werkzeug.utils import secure_filename
 
 from .invenio import run_record_upload
-from .utils import fill_invenio_metadata, form_to_json
+from .utils import fill_invenio_metadata, form_to_json, make_upload_tmpdir
 
 
 def _save_request_files(tmpdir):
@@ -54,7 +53,7 @@ def _save_files_and_extract_metadata(tmpdir):
 
 def extract_uploaded_file_metadata():
     """Extract file metadata from the current request's uploaded files."""
-    tmpdir = tempfile.mkdtemp(prefix="biosimdb_file_metadata_")
+    tmpdir = make_upload_tmpdir("biosimdb_file_metadata_")
     try:
         _, file_meta = _save_files_and_extract_metadata(tmpdir)
         return file_meta
@@ -109,7 +108,7 @@ def save_pending_submission(json_form=None):
         session["pending_files_dir"]: Set to temporary directory path containing
             uploaded files and optional ``simulation_metadata.json``.
     """
-    tmpdir = tempfile.mkdtemp(prefix="biosimdb_pending_")
+    tmpdir = make_upload_tmpdir("biosimdb_pending_")
     _, file_meta = _save_files_and_extract_metadata(tmpdir)
 
     if json_form is not None:
diff --git a/biosimdb_interface/form/utils.py b/biosimdb_interface/form/utils.py
index aab21ba..f77ea72 100644
--- a/biosimdb_interface/form/utils.py
+++ b/biosimdb_interface/form/utils.py
@@ -1,12 +1,22 @@
 #!/usr/bin/env python
 
 import copy
+import os
 import re
+import tempfile
+
+from flask import current_app
 
 from biosimdb_interface.schema.invenio import INVENIO_FORM_EMPTY
 from biosimdb_interface.schema.webform import get_simulation_metadata
 
 
+def make_upload_tmpdir(prefix):
+    upload_root = current_app.config["UPLOAD_FOLDER"]
+    os.makedirs(upload_root, exist_ok=True)
+    return tempfile.mkdtemp(prefix=prefix, dir=upload_root)
+
+
 def fill_invenio_metadata(form_data):
     """Populate a blank Invenio record with form data.