From bc4fc7d8e5b1f142f39cf60ef178ad7953033fa0 Mon Sep 17 00:00:00 2001
From: Luik <t.t.luik@amsterdamumc.nl>
Date: Tue, 13 Oct 2026 17:06:40 +0200
Subject: [PATCH] test: cover atomic canonical marker migration updates

---
 tests/test_canonical_marker_atomic.py | 85 +++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100644 tests/test_canonical_marker_atomic.py

diff --git a/tests/test_canonical_marker_atomic.py b/tests/test_canonical_marker_atomic.py
new file mode 100644
index 0000000..3b175b4
--- /dev/null
+++ b/tests/test_canonical_marker_atomic.py
@@ -0,0 +1,85 @@
+"""Regression coverage for canonical marker updates on CIFS-like mounts."""
+
+import ast
+import json
+import os
+from pathlib import Path
+from types import SimpleNamespace
+from unittest.mock import patch
+from uuid import uuid4
+
+import pytest
+
+
+SOURCE_ROOT = Path(os.environ.get(
+    "BIOMERO_SCRIPTS_ROOT", Path(__file__).parents[1]
+))
+SCRIPT = SOURCE_ROOT / "admin" / "BIOMERO_Migrate_Shallow_Storage.py"
+MARKER_NAME = ".biomero-canonical.json"
+
+
+def _marker_helpers():
+    tree = ast.parse(SCRIPT.read_text(encoding="utf-8"))
+    names = {"_write_json", "_canonical_marker_path", "_write_canonical_marker"}
+    nodes = [node for node in tree.body
+             if isinstance(node, ast.FunctionDef) and node.name in names]
+    namespace = {
+        "Path": Path,
+        "json": json,
+        "os": os,
+        "uuid4": uuid4,
+        "CANONICAL_MARKER_NAME": MARKER_NAME,
+        "external_canonical_marker_path": lambda path: path.parent / "external-marker",
+        "write_indexed_canonical_marker": lambda *args: pytest.fail(
+            "Existing marker must be updated, not created again"
+        ),
+    }
+    exec(compile(ast.Module(body=nodes, type_ignores=[]), str(SCRIPT), "exec"),
+         namespace)
+    assert names.issubset(namespace)
+    return namespace
+
+
+def test_existing_canonical_marker_is_replaced_without_direct_overwrite(tmp_path):
+    helpers = _marker_helpers()
+    store = tmp_path / "image.zarr"
+    store.mkdir()
+    marker = store / MARKER_NAME
+    marker.write_text(json.dumps({
+        "state": "committed", "markerSchema": 1,
+        "source": {"relativePath": "old"},
+    }), encoding="utf-8")
+    source = SimpleNamespace(to_dict=lambda: {"relativePath": "new"})
+    helpers["load_canonical_marker"] = lambda path: (
+        source if json.loads((path / MARKER_NAME).read_text(
+            encoding="utf-8"
+        ))["source"] == source.to_dict() else None
+    )
+    original_write_text = Path.write_text
+
+    def reject_direct_overwrite(path, *args, **kwargs):
+        if path == marker:
+            raise PermissionError(13, "Direct overwrite denied", str(path))
+        return original_write_text(path, *args, **kwargs)
+
+    with patch.object(Path, "write_text", reject_direct_overwrite):
+        helpers["_write_canonical_marker"](store, source)
+
+    assert json.loads(marker.read_text(encoding="utf-8"))["source"] == (
+        source.to_dict()
+    )
+    assert list(store.iterdir()) == [marker]
+
+
+def test_failed_replacement_preserves_marker_and_cleans_temp_file(tmp_path):
+    helpers = _marker_helpers()
+    marker = tmp_path / MARKER_NAME
+    original = '{"state": "committed", "source": "original"}'
+    marker.write_text(original, encoding="utf-8")
+
+    with patch.object(os, "replace", side_effect=PermissionError(13, "denied")):
+        with pytest.raises(PermissionError):
+            helpers["_write_json"](marker, {"source": "updated"})
+
+    assert marker.read_text(encoding="utf-8") == original
+    assert list(tmp_path.iterdir()) == [marker]