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-rw-r--r--quality_control/headers.py39
1 files changed, 39 insertions, 0 deletions
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())