[Bug]: [Errno 13] Permission denied on temp file during COD reference download (Windows)

[JonasWolf303]

Email (Optional)

j.wolf95@protonmail.com

Version

1.3.0

Which OS(es) are you using?

• MacOS
• Windows
• Linux

What happened?

On Windows, every reference-structure download during phase search fails with
[Errno 13] Permission denied on a temporary file. The server starts fine and
the web UI works; the failure occurs only when Dara fetches COD entries for the
search, e.g.:

Failed to download 9017498: [Errno 13] Permission denied: 'C:\Users\User1\AppData\Local\Temp\tmpyae69mru'

The same error repeats for other COD IDs, so no reference structures become
available and the search cannot proceed with database-retrieved phases.

To reproduce

1. Windows 10/11, Python <3.12.x, 64-bit> in a fresh venv
2. pip install dara-xrd (version <x.y.z>)
3. dara server
4. Open http://localhost:8898 and submit any pattern (tested with a
   two-column .xy, Cu radiation, precursor formulas spanning Bi–Fe–O)
5. Watch the server console during reference retrieval

Expected behavior

Reference CIFs download from COD and the search runs, as on Linux/macOS.

Actual behavior

Every download fails with [Errno 13] Permission denied on a file in the
user temp directory. Full console output:

<paste full traceback / log excerpt here>

What I ruled out

• Not folder permissions: redirected TMP/TEMP to a user-owned directory
  (C:\xrd\tmp) and restarted the server from the same shell — same error at
  the new location.
• Added an antivirus exclusion for the temp directory — no change.
• The machine has normal internet access (pip installs etc. work); the temp
  file is created, so this does not look like a network or ACL problem.

Suspected cause

This looks like the well-known Windows limitation with
tempfile.NamedTemporaryFile(delete=True): on Windows the file cannot be
reopened by name (e.g. by a download/parse step) while the creating handle is
still open, which raises exactly [Errno 13] Permission denied even though
permissions are fine. If the downloader writes to a NamedTemporaryFile and
then reopens it by path, that would reproduce this on every Windows machine
while working normally on Linux/macOS.

Possible fixes: delete=False with explicit cleanup, tempfile.mkstemp +
os.close before reuse, or downloading directly into the Dara cache/server
directory instead of the OS temp dir.

Environment

• OS: Windows <10/11, version>
• Python: <3.12.x> (64-bit, venv)
• dara-xrd: <x.y.z>
• Install: pip install dara-xrd, default MontyDB backend, default settings
• BGMN: <bundled / Profex-BGMN bundle x.y on PATH / not yet configured>

Additional context

Workaround for my use case would also be welcome: a way to supply local CIF
files as the reference set through the web UI / REST POST /api/submit, which
would bypass database retrieval entirely for closed chemical systems. If it
already exists, a pointer in the docs would help. Happy to test a patch on
Windows.

Code snippet

Log output

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