From 1b58d652e589eef400e8039f2dd2be6ac8d92029 Mon Sep 17 00:00:00 2001
From: "Gabriel A. Devenyi" <gdevenyi@gmail.com>
Date: Mon, 10 Aug 2026 13:47:41 -0400
Subject: [PATCH] Open the 2dseq memory map read-only

read_array maps a filesystem path with np.memmap and no mode. numpy's default
is "r+", so every dataset load asks the operating system for write access to the
raw data file. Nothing writes it: the array is copied out of the map on the same
line.

The consequence is that a dataset on a read-only file or mount cannot be loaded
at all -- which is how a shared scanner archive is normally exposed:

    PermissionError: [Errno 13] Permission denied: '.../2/pdata/1/2dseq'

The parameter files are unaffected, since those are opened in text mode, so the
failure looks selective: acqp, method, visu_pars and reco all read, and only the
binary fails, once per scan.

Reproduced by copying a PV6 study, chmod -R a-w, and loading it; on the same
file, mode="r+" raises and mode="r" reads all 1048576 values.

The archive branch below already reads through path.open("rb") and was never
affected.

test_dataset_reads_from_a_read_only_source covers it, in test_paths.py because
that module's study is synthetic and needs no corpus. It fails with
PermissionError without this change.
---
 brukerapi/paths.py |  7 ++++++-
 test/test_paths.py | 22 ++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/brukerapi/paths.py b/brukerapi/paths.py
index 1ffb23a..19fa031 100644
--- a/brukerapi/paths.py
+++ b/brukerapi/paths.py
@@ -71,9 +71,14 @@ def read_array(path, dtype, shape, order="F"):
     A filesystem path is memory-mapped as before. An archive member cannot be
     (a memory map cannot address a compressed member), so it degrades to a full
     read.
+
+    The map is opened read-only. numpy's default mode is "r+", which asks the
+    operating system for write access and so fails with EACCES on a read-only file
+    or mount -- the usual way a shared scanner archive is exposed. Nothing here
+    writes: the array is copied out on the same line.
     """
     if isinstance(path, (str, os.PathLike)):
-        return np.array(np.memmap(path, dtype=dtype, shape=shape, order=order)[:])
+        return np.array(np.memmap(path, dtype=dtype, mode="r", shape=shape, order=order)[:])
     with path.open("rb") as binary:
         buffer = binary.read()
     return np.frombuffer(buffer, dtype=dtype).reshape(shape, order=order)
diff --git a/test/test_paths.py b/test/test_paths.py
index febe765..4926c60 100644
--- a/test/test_paths.py
+++ b/test/test_paths.py
@@ -82,6 +82,28 @@ def test_dataset_reads_from_archive_identically(study_dir, study_zip):
     assert from_zip.shape_final == from_dir.shape_final
 
 
+def test_dataset_reads_from_a_read_only_source(study_dir):
+    """A dataset whose files are not writable must still load.
+
+    Scanner archives are normally exposed read-only, and nothing here writes: the
+    array is copied out of the map immediately. numpy's default memmap mode is
+    "r+", which asks the operating system for write access and fails with EACCES
+    on such a source, so the mode has to be given explicitly.
+    """
+    for path in sorted(study_dir.rglob("*")):
+        if path.is_file():
+            path.chmod(0o444)
+
+    try:
+        dataset = Dataset(study_dir / "1" / "pdata" / "1" / "2dseq", scale=False)
+        assert np.array_equal(dataset.data, DATA)
+    finally:
+        # restore, so pytest can clean the temporary directory up
+        for path in sorted(study_dir.rglob("*")):
+            if path.is_file():
+                path.chmod(0o644)
+
+
 def test_parameters_resolve_through_relative_paths(study_dir, study_zip):
     """``../../acqp`` resolves inside an archive, where ``..`` is not collapsed."""
     dataset = Dataset(study_zip / "1" / "pdata" / "1" / "2dseq", scale=False,