Enable user abortion of file parsing

Enable the user to abort the background parsing of the file.

1 files changed, 6 insertions, 2 deletions

diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index 5b1809b..9f8e8ee 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -4,7 +4,7 @@ import os
 import collections
 from enum import Enum
 from functools import partial
-from typing import Union, Iterable, Generator, Callable
+from typing import Iterable, Generator, Callable, Optional
 
 import quality_control.average as avg
 import quality_control.standard_error as se
@@ -65,7 +65,8 @@ def se_errors(line_number, fields):
 
 def collect_errors(
         filepath: str, filetype: FileType, strains: list,
-        update_progress: Union[Callable, None] = None) -> Generator:
+        update_progress: Optional[Callable] = None,
+        user_aborted: Optional[Callable] = lambda: False) -> Generator:
     """Run checks against file and collect all the errors"""
     errors = tuple()
     def __process_errors__(line_number, line, error_checker_fn, errors = tuple()):
@@ -80,6 +81,9 @@ def collect_errors(
 
     with open(filepath, encoding="utf-8") as input_file:
         for line_number, line in enumerate(input_file, start=1):
+            if user_aborted():
+                break
+
             if line_number == 1:
                 for error in __process_errors__(
                         line_number, line, partial(header_errors, strains=strains),