From 092ae35512b3ef236622c4ab9dfe2bafb221ded7 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 12 Feb 2024 13:03:35 +0300
Subject: Refactor: Use new decimal places checker.

---
 quality_control/checks.py | 18 ++++++++++++++++++
 r_qtl/r_qtl2_qc.py        | 26 ++++----------------------
 2 files changed, 22 insertions(+), 22 deletions(-)

diff --git a/quality_control/checks.py b/quality_control/checks.py
index 28b9ab5..475eb9e 100644
--- a/quality_control/checks.py
+++ b/quality_control/checks.py
@@ -2,6 +2,8 @@
 import re
 from typing import Optional
 
+from .errors import InvalidValue
+
 def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern:
     """
     Generate a regular expression for checking numbers
@@ -49,3 +51,19 @@ def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern:
         + r"}"
         + r")$"
     )
+
+def decimal_points_error(lineno: int,
+                         field: str,
+                         value: str,
+                         mini: int,
+                         maxi: Optional[int] = None) -> Optional[InvalidValue]:
+    """
+    Check that 'value' in a decimal number with the appropriate decimal places.
+    """
+    if not bool(decimal_places_pattern(mini, maxi).match(value)):
+        return InvalidValue(lineno, field, value, (
+            f"Invalid value '{value}'. Expected numerical value " +
+            f"with at least {mini} decimal places" +
+            (f" and at most {maxi} decimal places" if maxi is not None else "")
+            + "."))
+    return None
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index f62f142..aa5c81e 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -1,7 +1,6 @@
 """Quality control checks for R/qtl2 data bundles."""
-import re
 from zipfile import ZipFile
-from functools import reduce
+from functools import reduce, partial
 from typing import Union, Iterator, Optional, Callable
 
 from r_qtl import errors as rqe
@@ -10,6 +9,7 @@ from r_qtl.r_qtl2 import __FILE_TYPES__
 from r_qtl.fileerrors import MissingFile
 
 from quality_control.errors import InvalidValue
+from quality_control.checks import decimal_points_error
 
 def bundle_files_list(cdata: dict) -> tuple[tuple[str, str], ...]:
     """Retrieve files listed in control file."""
@@ -83,34 +83,16 @@ def geno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
 
 def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
     """Check for and retrieve pheno errors."""
-    def __min_3_decimal_places__(
-            lineno: int, field: str, value: str) -> Optional[InvalidValue]:
-        if not (re.search(r"^([0-9]+\.[0-9]{3,}|[0-9]+\.?0*)$", value)
-                or re.search(r"^0\.0+$", value)
-                or re.search("^0+$", value)):
-            return InvalidValue(lineno, field, value, (
-                f"Invalid value '{value}'. Expected numerical value "
-                "with at least 3 decimal places."))
-        return None
     return (
         error for error in retrieve_errors(
-            zfile, "pheno", (__min_3_decimal_places__,))
+            zfile, "pheno", (partial(decimal_points_error, mini=3),))
         if error is not None)
 
 def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]:
     """Check for and retrieve phenose errors."""
-    def __min_6_decimal_places__(
-            lineno: int, field: str, value: str) -> Optional[InvalidValue]:
-        if not (re.search(r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", value)
-                or re.search(r"^0\.0+$", value)
-                or re.search("^0+$", value)):
-            return InvalidValue(lineno, field, value, (
-                f"Invalid value '{value}'. Expected numerical value "
-                "with at least 6 decimal places."))
-        return None
     return (
         error for error in retrieve_errors(
-            zfile, "phenose", (__min_6_decimal_places__,))
+            zfile, "phenose", (partial(decimal_points_error, mini=6),))
         if error is not None)
 
 def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[
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