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-rw-r--r--quality_control/average.py7
-rw-r--r--quality_control/checks.py5
-rw-r--r--quality_control/errors.py6
-rw-r--r--quality_control/headers.py24
-rw-r--r--quality_control/parsing.py44
-rw-r--r--quality_control/standard_error.py11
6 files changed, 55 insertions, 42 deletions
diff --git a/quality_control/average.py b/quality_control/average.py
index ad732d0..bf288de 100644
--- a/quality_control/average.py
+++ b/quality_control/average.py
@@ -4,12 +4,13 @@ from typing import Union
from .utils import cell_error
from .errors import InvalidValue
-def invalid_value(line_number: int, column_number: int, val: str) -> Union[
- InvalidValue, None]:
+def invalid_value(
+ filename: str, line_number: int, column_number: int, val: str) -> Union[
+ InvalidValue, None]:
"""Return an `InvalidValue` object if `val` is not a valid "averages"
value."""
return cell_error(
- r"^([0-9]+\.[0-9]{3}|[0-9]+\.?0*)$", val, line=line_number,
+ r"^([0-9]+\.[0-9]{3}|[0-9]+\.?0*)$", val, filename=filename, line=line_number,
column=column_number, value=val, message=(
f"Invalid value '{val}'. "
"Expected string representing a number with exactly three "
diff --git a/quality_control/checks.py b/quality_control/checks.py
index 475eb9e..bdfd12b 100644
--- a/quality_control/checks.py
+++ b/quality_control/checks.py
@@ -52,7 +52,8 @@ def decimal_places_pattern(mini: int, maxi: Optional[int] = None) -> re.Pattern:
+ r")$"
)
-def decimal_points_error(lineno: int,
+def decimal_points_error(filename: str,# pylint: disable=[too-many-arguments]
+ lineno: int,
field: str,
value: str,
mini: int,
@@ -61,7 +62,7 @@ def decimal_points_error(lineno: int,
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, (
+ return InvalidValue(filename, 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 "")
diff --git a/quality_control/errors.py b/quality_control/errors.py
index fff6c7c..01afa81 100644
--- a/quality_control/errors.py
+++ b/quality_control/errors.py
@@ -3,10 +3,10 @@
from collections import namedtuple
InvalidValue = namedtuple(
- "InvalidValue", ("line", "column", "value", "message"))
+ "InvalidValue", ("filename", "line", "column", "value", "message"))
DuplicateHeading = namedtuple(
- "DuplicateHeading", ("line", "columns", "heading", "message"))
+ "DuplicateHeading", ("filename", "line", "columns", "heading", "message"))
InconsistentColumns = namedtuple(
- "InconsistentColumns", ("line", "header_count", "contents_count", "message"))
+ "InconsistentColumns", ("filename", "line", "header_count", "contents_count", "message"))
diff --git a/quality_control/headers.py b/quality_control/headers.py
index f4f4dad..436ea5a 100644
--- a/quality_control/headers.py
+++ b/quality_control/headers.py
@@ -5,30 +5,34 @@ from typing import Union, Tuple, Sequence
from quality_control.errors import InvalidValue, DuplicateHeading
-def invalid_header(
- line_number: int, headers: Sequence[str]) -> Union[InvalidValue, None]:
+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(
- line_number, 0, "<TAB>".join(headers),
+ filename, line_number, 0, "<TAB>".join(headers),
"The header MUST contain at least 2 columns")
return None
def invalid_headings(
- line_number: int, strains: Sequence[str],
+ 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(
- line_number, col, header, f"'{header}' not a valid strain.")
+ 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(
- line_number: int,
- headers: Sequence[str]) -> Tuple[DuplicateHeading, ...]:
+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):
@@ -42,7 +46,7 @@ def duplicate_headings(
}
return tuple(
DuplicateHeading(
- line_number, columns, heading, (
+ 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())
diff --git a/quality_control/parsing.py b/quality_control/parsing.py
index f7a664f..f1d21fc 100644
--- a/quality_control/parsing.py
+++ b/quality_control/parsing.py
@@ -1,6 +1,7 @@
"""Module handling the high-level parsing of the files"""
import collections
from enum import Enum
+from pathlib import Path
from functools import partial
from typing import Tuple, Union, Generator, Callable, Optional
@@ -30,44 +31,44 @@ def strain_names(dbconn: mdb.Connection, speciesid: int) -> tuple[str, ...]:
lambda item: bool(item.strip() if item is not None else item),
(name for names in samplenames for name in names))))
-def header_errors(line_number, fields, strains):
+def header_errors(filename, line_number, fields, strains):
"""Gather all header row errors."""
return (
- (invalid_header(line_number, fields),) +
- invalid_headings(line_number, strains, fields[1:]) +
- duplicate_headings(line_number, fields))
+ (invalid_header(filename, line_number, fields),) +
+ invalid_headings(filename, line_number, strains, fields[1:]) +
+ duplicate_headings(filename, line_number, fields))
-def empty_value(line_number, column_number, value):
+def empty_value(filename, line_number, column_number, value):
"""Check for empty field values."""
if value == "":
- return InvalidValue(
- line_number, column_number, value, "Empty value for column")
+ return InvalidValue(filename, line_number, column_number, value,
+ "Empty value for column")
return None
-def average_errors(line_number, fields):
+def average_errors(filename, line_number, fields):
"""Gather all errors for a line in a averages file."""
return (
- (empty_value(line_number, 1, fields[0]),) +
+ (empty_value(filename, line_number, 1, fields[0]),) +
tuple(
- avg.invalid_value(line_number, *field)
+ avg.invalid_value(filename, line_number, *field)
for field in enumerate(fields[1:], start=2)))
-def se_errors(line_number, fields):
+def se_errors(filename, line_number, fields):
"""Gather all errors for a line in a standard-errors file."""
return (
- (empty_value(line_number, 1, fields[0]),) +
+ (empty_value(filename, line_number, 1, fields[0]),) +
tuple(
- se.invalid_value(line_number, *field)
+ se.invalid_value(filename, line_number, *field)
for field in enumerate(fields[1:], start=2)))
-def make_column_consistency_checker(header_row):
+def make_column_consistency_checker(filename, header_row):
"""Build function to check for column consistency"""
headers = tuple(field.strip() for field in header_row.split("\t"))
def __checker__(line_number, contents_row):
contents = tuple(field.strip() for field in contents_row.split("\t"))
if len(contents) != len(headers):
return InconsistentColumns(
- line_number, len(headers), len(contents),
+ filename, line_number, len(headers), len(contents),
(f"Header row has {len(headers)} columns while row "
f"{line_number} has {len(contents)} columns"))
return None
@@ -79,8 +80,10 @@ def collect_errors(
user_aborted: Callable = lambda: False) -> Generator:
"""Run checks against file and collect all the errors"""
errors:Tuple[Union[InvalidValue, DuplicateHeading], ...] = tuple()
- def __process_errors__(line_number, line, error_checker_fn, errors = tuple()):
+ def __process_errors__(
+ filename, line_number, line, error_checker_fn, errors = tuple()):
errs = error_checker_fn(
+ filename,
line_number,
tuple(field.strip() for field in line.split("\t")))
if errs is None:
@@ -90,6 +93,7 @@ def collect_errors(
return errors + (errs,)
with open_file(filepath) as input_file:
+ filename = Path(filepath).name
for line_number, line in enumerate(input_file, start=1):
if user_aborted():
break
@@ -98,9 +102,11 @@ def collect_errors(
line = line.decode("utf-8")
if line_number == 1:
- consistent_columns_checker = make_column_consistency_checker(line)
+ consistent_columns_checker = make_column_consistency_checker(
+ filename, line)
for error in __process_errors__(
- line_number, line, partial(header_errors, strains=strains),
+ filename, line_number, line,
+ partial(header_errors, strains=strains),
errors):
yield error
@@ -110,7 +116,7 @@ def collect_errors(
yield col_consistency_error
for error in __process_errors__(
- line_number, line, (
+ filename, line_number, line, (
average_errors if filetype == FileType.AVERAGE
else se_errors),
errors):
diff --git a/quality_control/standard_error.py b/quality_control/standard_error.py
index 90beb8a..00b1ac6 100644
--- a/quality_control/standard_error.py
+++ b/quality_control/standard_error.py
@@ -4,17 +4,18 @@ from typing import Union
from .utils import cell_error
from .errors import InvalidValue
-def invalid_value(
- line_number: int, column_number: int, val: str) -> Union[
- InvalidValue, None]:
+def invalid_value(filename: str,
+ 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`.
"""
return cell_error(
- r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, line=line_number,
- column=column_number, value=val, message=(
+ r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", val, filename=filename,
+ line=line_number, column=column_number, value=val, message=(
f"Invalid value '{val}'. "
"Expected string representing a number with at least six "
"decimal places."))
generated by cgit v1.2.3 (git 2.25.4) at 2024-07-04 22:34:14 +0000