FIX wsl conversion

alphadia/cli.py

@@ -170,14 +170,14 @@ def parse_output_directory(args: argparse.Namespace, config: dict) -> str:
  output_directory = None
  if "output_directory" in config:
  output_directory = (
- utils.wsl_to_windows(config["output_directory"])
+ utils.windows_to_wsl(config["output_directory"])
  if args.wsl
  else config["output_directory"]
  )
 
  if args.output is not None:
  output_directory = (
- utils.wsl_to_windows(args.output) if args.wsl else args.output
+ utils.windows_to_wsl(args.output) if args.wsl else args.output
  )
 
  return output_directory
@@ -205,13 +205,13 @@ def parse_raw_path_list(args: argparse.Namespace, config: dict) -> list:
  """
  config_raw_path_list = config["raw_path_list"] if "raw_path_list" in config else []
  raw_path_list = (
- utils.wsl_to_windows(config_raw_path_list) if args.wsl else config_raw_path_list
+ utils.windows_to_wsl(config_raw_path_list) if args.wsl else config_raw_path_list
  )
- raw_path_list += utils.wsl_to_windows(args.file) if args.wsl else args.file
+ raw_path_list += utils.windows_to_wsl(args.file) if args.wsl else args.file
 
  config_directory = config["directory"] if "directory" in config else None
- directory = utils.wsl_to_windows(config_directory) if args.wsl else config_directory
- directory = utils.wsl_to_windows(args.directory) if args.wsl else args.directory
+ directory = utils.windows_to_wsl(config_directory) if args.wsl else config_directory
+ directory = utils.windows_to_wsl(args.directory) if args.wsl else args.directory
 
  if directory is not None:
  raw_path_list += [os.path.join(directory, f) for f in os.listdir(directory)]
@@ -253,11 +253,11 @@ def parse_library(args: argparse.Namespace, config: dict) -> str:
  library = None
  if "library" in config:
  library = (
- utils.wsl_to_windows(config["library"]) if args.wsl else config["library"]
+ utils.windows_to_wsl(config["library"]) if args.wsl else config["library"]
  )
 
  if args.library is not None:
- library = utils.wsl_to_windows(args.library) if args.wsl else args.library
+ library = utils.windows_to_wsl(args.library) if args.wsl else args.library
 
  return library
 
@@ -285,11 +285,11 @@ def parse_fasta(args: argparse.Namespace, config: dict) -> list:
 
  config_fasta_path_list = config["fasta_list"] if "fasta_list" in config else []
  fasta_path_list = (
- utils.wsl_to_windows(config_fasta_path_list)
+ utils.windows_to_wsl(config_fasta_path_list)
  if args.wsl
  else config_fasta_path_list
  )
- fasta_path_list += utils.wsl_to_windows(args.fasta) if args.wsl else args.fasta
+ fasta_path_list += utils.windows_to_wsl(args.fasta) if args.wsl else args.fasta
 
  return fasta_path_list
 

alphadia/utils.py

@@ -2,6 +2,7 @@
 import logging
 from ctypes import Structure, c_double
 import typing
+import re
 
 # alphadia imports
 
@@ -66,11 +67,51 @@ def wsl_to_windows(
 
  """
  if isinstance(path, str):
- return path.replace("/mnt/", "").replace("/", "\\")
+
+ disk_match = re.search(r'^/mnt/[a-z]', path)
+
+ if len(disk_match.group()) == 0:
+ raise ValueError('Could not find disk in path during wsl to windows conversion')
+
+ disk_letter = disk_match.group()[5].upper()
+
+ return re.sub(r'^/mnt/[a-z]', f'{disk_letter}:', path).replace('/', '\\')
+
  elif isinstance(path, (list, tuple)):
  return [wsl_to_windows(p) for p in path]
  else:
  raise ValueError(f"Unsupported type {type(path)}")
+
+def windows_to_wsl(
+ path: typing.Union[str, list, tuple]
+) -> typing.Union[str, list, tuple]:
+ """Converts a Windows path to a WSL path.
+
+ Parameters
+ ----------
+ path : str, list, tuple
+ Windows path.
+
+ Returns
+ -------
+ str, list, tuple
+ WSL path.
+
+ """
+ if isinstance(path, str):
+ disk_match = re.search(r'^[A-Z]:', path)
+
+ if len(disk_match.group()) == 0:
+ raise ValueError('Could not find disk in path during windows to wsl conversion')
+
+ disk_letter = disk_match.group()[0].lower()
+
+ return re.sub(r'^[A-Z]:', f'/mnt/{disk_letter}', path.replace('\\', '/'))
+
+ elif isinstance(path, (list, tuple)):
+ return [windows_to_wsl(p) for p in path]
+ else:
+ raise ValueError(f"Unsupported type {type(path)}")
 
 
 def recursive_update(full_dict: dict, update_dict: dict):

tests/unit_tests/test_utils.py

@@ -5,7 +5,7 @@
 import unittest
 
 # local
-from alphadia.utils import amean0, amean1, calculate_score_groups
+from alphadia.utils import amean0, amean1, calculate_score_groups, wsl_to_windows, windows_to_wsl
 
 
 # global
@@ -88,3 +88,17 @@ def test_score_groups():
  assert np.allclose(
  sample_df["score_group_idx"].values, np.array([0, 0, 1, 1, 2, 3, 4, 4, 5, 5])
  )
+
+
+def test_wsl_conversion():
+ test_path = "/mnt/c/Users/username/Documents/test.txt"
+ expected_path = "C:\\Users\\username\\Documents\\test.txt"
+
+ assert wsl_to_windows(test_path) == expected_path
+ assert windows_to_wsl(expected_path) == test_path
+
+ test_path = "/mnt/d/Users/us__.sdername/D ocuments/test.txt"
+ expected_path = "D:\\Users\\us__.sdername\\D ocuments\\test.txt"
+
+ assert wsl_to_windows(test_path) == expected_path
+ assert windows_to_wsl(expected_path) == test_path