validate_paths data prefix

ark/utils/io_utils.py

@@ -3,7 +3,7 @@
 import warnings
 
 
-def validate_paths(paths, data_prefix=True):
+def validate_paths(paths, data_prefix=False):
     """Verifys that paths exist and don't leave Docker's scope
 
     Args:
@@ -22,20 +22,21 @@ def validate_paths(paths, data_prefix=True):
         paths = [paths]
 
     for path in paths:
+        # check data prefix
+        if data_prefix and not str(path).startswith('../data'):
+            raise ValueError(
+                f'The path, {path}, is not prefixed with \'../data\'.\n'
+                f'Be sure to add all images/files/data to the \'data\' folder, '
+                f'and to reference as \'../data/path_to_data/myfile.tif\'')
+
         if not os.path.exists(path):
-            if str(path).startswith('../data') or not data_prefix:
-                for parent in reversed(pathlib.Path(path).parents):
-                    if not os.path.exists(parent):
-                        raise ValueError(
-                            f'A bad path, {path}, was provided.\n'
-                            f'The folder, {parent.name}, could not be found...')
-                raise ValueError(
-                    f'The file/path, {pathlib.Path(path).name}, could not be found...')
-            else:
-                raise ValueError(
-                    f'The path, {path}, is not prefixed with \'../data\'.\n'
-                    f'Be sure to add all images/files/data to the \'data\' folder, '
-                    f'and to reference as \'../data/path_to_data/myfile.tif\'')
+            for parent in reversed(pathlib.Path(path).parents):
+                if not os.path.exists(parent):
+                    raise ValueError(
+                        f'A bad path, {path}, was provided.\n'
+                        f'The folder, {parent.name}, could not be found...')
+            raise ValueError(
+                f'The file/path, {pathlib.Path(path).name}, could not be found...')
 
 
 def list_files(dir_name, substrs=None, exact_match=False, ignore_hidden=True):

ark/utils/io_utils_test.py

@@ -36,26 +36,31 @@ def test_validate_paths():
         wrong_file = os.path.join(valid_path + '/real_subdirectory', 'not_a_real_file.tiff')
 
         # test one valid path
-        iou.validate_paths(valid_path)
+        iou.validate_paths(valid_path, data_prefix=True)
 
         # test multiple valid paths
-        iou.validate_paths([valid_path, '../data', valid_path + '/real_subdirectory'])
+        iou.validate_paths([valid_path, '../data', valid_path + '/real_subdirectory'],
+                           data_prefix=True)
 
         # test out-of-scope
         with pytest.raises(ValueError, match=r".*not_a_real_directory.*prefixed.*"):
-            iou.validate_paths(starts_out_of_scope)
+            iou.validate_paths(starts_out_of_scope, data_prefix=True)
 
         # test mid-directory existence
         with pytest.raises(ValueError, match=r".*bad path.*not_a_real_subdirectory.*"):
-            iou.validate_paths(bad_middle_path)
+            iou.validate_paths(bad_middle_path, data_prefix=True)
 
         # test file existence
         with pytest.raises(ValueError, match=r".*The file/path.*not_a_real_file.*"):
-            iou.validate_paths(wrong_file)
+            iou.validate_paths(wrong_file, data_prefix=True)
 
     # make tempdir for testing outside of docker
     with tempfile.TemporaryDirectory() as valid_path:
 
+        # check valid path but no data prefix
+        with pytest.raises(ValueError, match=r".*is not prefixed with.*"):
+            iou.validate_paths(valid_path, data_prefix=True)
+
         # make valid subdirectory
         valid_parts = [p for p in pathlib.Path(valid_path).parts]
         valid_parts[0] = 'not_a_real_directory'