1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
"""Validate the headers"""
from functools import reduce
from typing import Union, Tuple, Sequence
from quality_control.errors import InvalidValue, DuplicateHeading
def invalid_header(filename: str,
line_number: int,
headers: Sequence[str]) -> Union[InvalidValue, None]:
"""Return an `InvalidValue` object if the header row has less than 2
items."""
if len(headers) < 2:
return InvalidValue(
filename, line_number, 0, "<TAB>".join(headers),
"The header MUST contain at least 2 columns")
return None
def invalid_headings(
filename: str, line_number: int, strains: Sequence[str],
headings: Sequence[str]) -> Union[Tuple[InvalidValue, ...], None]:
"""Return tuple of `InvalidValue` objects for each error found for every
column heading."""
return tuple(
InvalidValue(filename,
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(filename: str,
line_number: int,
headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]:
"""Return a tuple of `DuplicateHeading` objects for each column heading that
is a duplicate of another column heading."""
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 = {# type: ignore[var-annotated]
heading: columns for heading, columns in
reduce(__update_columns__, enumerate(headers, start=1), {}).items()
if len(columns) > 1
}
return tuple(
DuplicateHeading(
filename, line_number, columns, heading, (
f"Heading '{heading}', is repeated in columns "
f"{','.join(str(i) for i in columns)}"))
for heading, columns in repeated.items())
|
