Extract progress indication from the parsing

Since progress indication is not part of the parsing, this commit
extracts the progress indication into functions with well defined
input arguments that hide the progress indication logic from the
parsing function.

3 files changed, 39 insertions, 14 deletions

diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index 655b98a..5b1809b 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -65,7 +65,7 @@ def se_errors(line_number, fields):
 
 def collect_errors(
         filepath: str, filetype: FileType, strains: list,
-        updater: Union[Callable, None] = None) -> Generator:
+        update_progress: Union[Callable, None] = None) -> Generator:
     """Run checks against file and collect all the errors"""
     errors = tuple()
     def __process_errors__(line_number, line, error_checker_fn, errors = tuple()):
@@ -78,8 +78,6 @@ def collect_errors(
             return errors + tuple(error for error in errs if error is not None)
         return errors + (errs,)
 
-    filesize = os.stat(filepath).st_size
-    processed_size = 0
     with open(filepath, encoding="utf-8") as input_file:
         for line_number, line in enumerate(input_file, start=1):
             if line_number == 1:
@@ -96,12 +94,8 @@ def collect_errors(
                         errors):
                     yield error
 
-            processed_size = processed_size + len(line)
-            if updater:
-                updater({
-                    "line_number": line_number,
-                    "percent": (processed_size/filesize) * 100
-                })
+            if update_progress:
+                update_progress(line_number, line)
 
 def take(iterable: Iterable, num: int) -> list:
     """Take at most `num` items from `iterable`."""
diff --git a/quality_control/utils.py b/quality_control/utils.py
new file mode 100644
index 0000000..0072608
--- /dev/null
+++ b/quality_control/utils.py
@@ -0,0 +1,21 @@
+"""Utilities that might be useful elsewhere."""
+
+from collections import namedtuple
+
+ProgressIndicator = namedtuple(
+    "ProgressIndicator", ("filesize", "processedsize", "currentline", "percent"))
+
+def make_progress_calculator(filesize: int):
+    """
+    Returns a function that takes two arguments, `linenumber` and `linetext` and
+    return a `ProgressIndicator` object with the computed progress.
+    """
+    processedsize = 0
+    def __calculator__(linenumber: int, linetext: str) -> ProgressIndicator:
+        nonlocal processedsize
+        processedsize = processedsize + len(linetext)
+        return ProgressIndicator(
+            filesize, processedsize, linenumber,
+            ((processedsize/filesize) * 100))
+
+    return __calculator__
diff --git a/scripts/qc.py b/scripts/qc.py
index 9d57f4b..9bad55e 100644
--- a/scripts/qc.py
+++ b/scripts/qc.py
@@ -2,10 +2,12 @@
 import os
 import sys
 import argparse
+from typing import Union, Callable
 
 import magic
 
 from quality_control.errors import InvalidValue
+from quality_control.utils import make_progress_calculator
 from quality_control.parsing import (
     take,
     FileType,
@@ -54,10 +56,18 @@ def cli_argument_parser():
         default=False, action="store_true")
     return parser
 
-def progress_indicator(msg):
+def make_progress_indicator(
+        verbose: bool, progress_calc_fn: Callable) -> Union[Callable, None]:
     """Utility to display the progress"""
-    print(f"LINE: {msg['line_number']} ({msg['percent']:.2f}%)", end="\r")
-    return msg
+    if not verbose:
+        return None
+
+    def __indicator__(linenumber, linetext):
+        msg = progress_calc_fn(linenumber, linetext)
+        print(f"LINE: {msg.currentline} ({msg.percent:.2f}%)", end="\r")
+        return msg
+
+    return __indicator__
 
 def print_errors(errors, verbose):
     """Print out the errors"""
@@ -78,8 +88,8 @@ def print_errors(errors, verbose):
 
 def check(filepath, filetype, strains, count, verbose=False):
     """Check the file and print out results"""
-    if verbose:
-        updater = progress_indicator
+    updater = make_progress_indicator(
+        verbose, make_progress_calculator(os.stat(filepath).st_size))
 
     if count > 0:
         return print_errors(