Return errors when found or None otherwise

This commit adds a number of functions that return the error object
when an error is found, or `None` otherwise. It avoids the use of
exceptions as control flow constructs.

4 files changed, 76 insertions, 0 deletions

diff --git a/quality_control/average.py b/quality_control/average.py
index 2907b9c..9ca16a9 100644
--- a/quality_control/average.py
+++ b/quality_control/average.py
@@ -1,6 +1,8 @@
 """Contain logic for checking average files"""
 import re
+from typing import Union
 
+from .errors import InvalidValue
 from .errors import InvalidCellValue
 
 def valid_value(val):
@@ -11,3 +13,13 @@ def valid_value(val):
         f"Invalid value '{val}'. "
         "Expected string representing a number with exactly three decimal "
         "places.")
+
+def invalid_value(line_number: int, column_number: int, val: str) -> Union[
+        InvalidValue, None]:
+    if re.search(r"^[0-9]+\.[0-9]{3}$", val):
+        return None
+    return InvalidValue(
+        line_number, column_number, val, (
+            f"Invalid value '{val}'. "
+            "Expected string representing a number with exactly three decimal "
+            "places."))
diff --git a/quality_control/errors.py b/quality_control/errors.py
index 29a38f9..1eda646 100644
--- a/quality_control/errors.py
+++ b/quality_control/errors.py
@@ -1,5 +1,7 @@
 """Hold exceptions for QC package"""
 
+from collections import namedtuple
+
 class InvalidCellValue(Exception):
     """Raised when a function encounters an invalid value"""
 
@@ -22,3 +24,9 @@ class ParseError(Exception):
     """Raised if any of the above exceptions are raised"""
     def __init__(self, *args):
         super().__init__(*args)
+
+InvalidValue = namedtuple(
+    "InvalidValue", ("line_number", "column_number", "value", "message"))
+
+DuplicateHeading = namedtuple(
+    "InvalidValue", ("line_number", "heading", "columns","message"))
diff --git a/quality_control/headers.py b/quality_control/headers.py
index b7bc01e..a5a5065 100644
--- a/quality_control/headers.py
+++ b/quality_control/headers.py
@@ -1,5 +1,9 @@
 """Validate the headers"""
 
+from functools import reduce
+from typing import Union, Tuple, Sequence
+
+from quality_control.errors import InvalidValue, DuplicateHeading
 from quality_control.errors import DuplicateHeader, InvalidHeaderValue
 
 def valid_header(strains, headers):
@@ -23,3 +27,38 @@ def valid_header(strains, headers):
             for header, times in repeated))
 
     return headers
+
+
+def invalid_header(
+        line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]:
+    if len(headers) < 2:
+        return InvalidValue(
+            line_number, 0, "<TAB>".join(headers),
+            "The header MUST contain at least 2 columns")
+
+def invalid_headings(
+        line_number: int, strains: Sequence[str],
+        headings: Sequence[str]) -> Union[Tuple[InvalidValue, ...], None]:
+    return tuple(
+        InvalidValue(
+            line_number, col, header, f"'{header}' not a valid strain.")
+        for col, header in
+        enumerate(headings, start=2) if header not in strains)
+
+def duplicate_headings(
+        line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]:
+    def __update_columns__(acc, item):
+        if item[1] in acc.keys():
+            return {**acc, item[1]: acc[item[1]] + (item[0],)}
+        return {**acc, item[1]: (item[0],)}
+    repeated = {
+        heading: columns for heading, columns in
+        reduce(__update_columns__, enumerate(headers, start=1), dict()).items()
+        if len(columns) > 1
+    }
+    return tuple(
+        DuplicateHeading(
+            line_number, heading, columns, (
+                f"Heading '{heading}', is repeated in columns "
+                f"{','.join(str(i) for i in columns)}"))
+        for heading, columns in repeated.items())
diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index f1e33c4..022cc9b 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -1,6 +1,8 @@
 """Contain logic for checking standard error files"""
 import re
+from typing import Union
 
+from .errors import InvalidValue
 from .errors import InvalidCellValue
 
 def valid_value(val):
@@ -11,3 +13,18 @@ def valid_value(val):
         f"Invalid value '{val}'. "
         "Expected string representing a number with at least six decimal "
         "places.")
+
+def invalid_value(line_number: int, column_number: int, val: str) -> Union[
+        InvalidValue, None]:
+    """
+    Returns a `quality_control.errors.InvalidValue` object in the case where
+    `val` is not a valid input for standard error files, otherwise, it returns
+    `None`.
+    """
+    if re.search(r"^[0-9]+\.[0-9]{6,}$", val):
+        return None
+    return InvalidValue(
+        line_number, column_number, val, (
+            f"Invalid value '{val}'. "
+            "Expected string representing a number with at least six decimal "
+            "places."))