Close the file handler if the file is corrupt. (#42)

* Trying to make a correctly failing test

* Implemented assert_file_not_in_use

* Updated the linux test script

* Another try for linux

* Fixed the line for linux

* Make sure the test is failing

* Make sure the file is closed if ValueError

sif_parser/sif_open.py

@@ -28,8 +28,12 @@ def np_open(sif_file, ignore_corrupt=False, lazy=None):
         tile, size, no_images, info = _open(f)
     except AttributeError:
         f = open(sif_file,'rb')
-        tile, size, no_images, info = _open(f)
         will_close = True
+        try:
+            tile, size, no_images, info = _open(f)
+        except SyntaxError as e:
+            f.close()
+            raise e
 
     # allocate np.array
     if lazy == 'dask':
@@ -72,6 +76,8 @@ def np_open(sif_file, ignore_corrupt=False, lazy=None):
         except ValueError:
             data = data[:i]
             if not ignore_corrupt:
+                if will_close:
+                    f.close()
                 raise ValueError(
                     'The file might be corrupt. Number of files should be {} '
                     'according to the header, but only {} is found in the file.'

testings/test_open.py

@@ -2,6 +2,8 @@
 import sys
 import glob
 import codecs
+import psutil
+
 
 THIS_DIR = os.path.dirname(__file__)
 sys.path.append(THIS_DIR + "/../sif_parser/")
@@ -49,6 +51,30 @@
         )
 
 
+def is_file_not_in_use(filename):
+    platform = sys.platform
+    if platform == "linux":
+        for proc in psutil.process_iter():
+            try:
+                for item in proc.open_files():
+                    if filename == item.path:
+                        return False
+            except Exception:
+                pass
+        return True
+    elif platform == "darwin":
+        raise NotImplementedError('Testing in Mac is not supported.')
+    elif platform == "win32":
+        # for windows:
+        try:
+            os.rename(filename, filename)
+        except Exception:
+            return False
+        return True
+    else:
+        raise Exception("OS not supported")
+
+
 def test_step_and_glue():
     filename = THIS_DIR + "/step_and_glue/step_and_glue.sif"
     with open(filename, "rb") as f:
@@ -191,6 +217,9 @@ def test_corrupt_file(filename):
     with pytest.raises(ValueError) as e_info:
         data, info = sif_parser.np_open(filename)
 
+    # try open with a write mode to make sure the file is closed
+    assert is_file_not_in_use(filename)
+
     with pytest.warns(UserWarning, match="corrupt."):
         data, info = sif_parser.np_open(filename, ignore_corrupt=True)