Preserve trailing underscores (#676)

* Streamlined logic for 'secure_path', and added logic to preserve trailing underscores in file path parts
* Added unit tests for 'secure_path'

Author: tieneupin

src/murfey/util/__init__.py

@@ -27,24 +27,18 @@ def sanitise_nonpath(in_string: str) -> str:
 
 
 def secure_path(in_path: Path, keep_spaces: bool = False) -> Path:
-    if keep_spaces:
-        secured_parts = []
-        for p, part in enumerate(in_path.parts):
-            if " " in part:
-                secured_parts.append(part)
-            elif ":" in part and not p:
-                secured_parts.append(secure_filename(part) + ":")
-            else:
-                secured_parts.append(secure_filename(part))
-    else:
-        secured_parts = [
-            (
-                secure_filename(part) + ":"
-                if p == 0 and ":" in part
-                else secure_filename(part)
-            )
-            for p, part in enumerate(in_path.parts)
-        ]
+    secured_parts = []
+    for p, part in enumerate(in_path.parts):
+        if p == 0 and ":" in part:
+            secured_parts.append(secure_filename(part) + ":")
+        elif " " in part and keep_spaces:
+            secured_parts.append(part)
+        elif part.endswith("_"):
+            # Preserve all trailing underscores
+            num_underscores = len(part) - len(part.rstrip("_"))
+            secured_parts.append(secure_filename(part) + (num_underscores * "_"))
+        else:
+            secured_parts.append(secure_filename(part))
     return Path("/".join(secured_parts))
 
 

tests/util/test_init.py

@@ -0,0 +1,63 @@
+"""
+Test module for the functions located in murfey.util.__init__
+"""
+
+from pathlib import Path
+
+import pytest
+
+from murfey.util import secure_path
+
+secure_path_test_matrix = (
+    # Keep spaces? | Input path | Expected output
+    # Tomo workflow examples
+    (
+        False,
+        "D:/User_22220202_090000_cm40000-1/Position_1_1_001_0.00_22220202_090000_EER.eer",
+        "D:/User_22220202_090000_cm40000-1/Position_1_1_001_0.00_22220202_090000_EER.eer",
+    ),
+    (
+        False,
+        "D:/User_22220202_090000_cm40000-1_/Position_1_1_001_0.00_22220202_090000_EER.eer",
+        "D:/User_22220202_090000_cm40000-1_/Position_1_1_001_0.00_22220202_090000_EER.eer",
+    ),
+    # CLEM workflow examples
+    (
+        True,
+        "D:/Session/cm40000-1/images/My Sample/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+        "D:/Session/cm40000-1/images/My Sample/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+    ),
+    (
+        True,
+        "D:/Session/cm40000-1/images/My Sample_/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+        "D:/Session/cm40000-1/images/My Sample_/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+    ),
+    (
+        True,
+        "D:/Session/cm40000-1/images/My_Sample_/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+        "D:/Session/cm40000-1/images/My_Sample_/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+    ),
+    # Go wild
+    (
+        True,
+        "D:/some path/to_/this/repo!/my_file.txt",
+        "D:/some path/to_/this/repo/my_file.txt",
+    ),
+    (
+        True,
+        "D:/some path__/to_/this/repo/my file.txt",
+        "D:/some path__/to_/this/repo/my file.txt",
+    ),
+    (
+        False,
+        "D:/some path__/to_/this/repo/my file.txt",
+        "D:/some_path__/to_/this/repo/my_file.txt",
+    ),
+)
+
+
+@pytest.mark.parametrize("test_params", secure_path_test_matrix)
+def test_secure_path(test_params: tuple[bool, str, str]):
+    # Unpack test params
+    keep_spaces, input_path, expected_output = test_params
+    assert secure_path(Path(input_path), keep_spaces) == Path(expected_output)