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-rw-r--r--quality_control/average.py12
-rw-r--r--quality_control/errors.py8
-rw-r--r--quality_control/headers.py39
-rw-r--r--quality_control/standard_error.py17
-rw-r--r--tests/qc/test_cells.py85
-rw-r--r--tests/qc/test_header.py58
6 files changed, 217 insertions, 2 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."))
diff --git a/tests/qc/test_cells.py b/tests/qc/test_cells.py
index d4ef911..46aeb64 100644
--- a/tests/qc/test_cells.py
+++ b/tests/qc/test_cells.py
@@ -1,12 +1,18 @@
"""Test that values in cells within a line fulfill the required criteria"""
import pytest
+from random import randint
from hypothesis import given
from hypothesis import strategies as st
+from quality_control.errors import InvalidValue
from quality_control.errors import InvalidCellValue
-from quality_control.average import valid_value as avg_valid_value
-from quality_control.standard_error import valid_value as se_valid_value
+from quality_control.average import (
+ valid_value as avg_valid_value,
+ invalid_value as avg_invalid_value)
+from quality_control.standard_error import (
+ valid_value as se_valid_value,
+ invalid_value as se_invalid_value)
@given(num_str=st.from_regex(
r"^(?!([0-9]+\.([0-9]{3}|[0-9]{6,}))).*", fullmatch=True))
@@ -51,3 +57,78 @@ def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str):
assert (
isinstance(processed, float) and
processed == float(num_str))
+
+## ================================================================================
+
+@given(num_str=st.from_regex(
+ r"^(?!([0-9]+\.([0-9]{3}|[0-9]{6,}))).*", fullmatch=True))
+def test_cell_value_errors_with_invalid_inputs2(num_str):
+ """
+ GIVEN: `num_str` is an arbitrary string that is an invalid input,
+ WHEN: `num_str` is provided as an argument to `*_invalid_value` functions,
+ THEN: The `*_invalid_value` functions return a
+ `quality_control.errors.InvalidValue` object which holds the error
+ information.
+ """
+ assert avg_invalid_value(0, 0, num_str) == InvalidValue(
+ 0, 0, num_str, (
+ f"Invalid value '{num_str}'. Expected string representing a number "
+ "with exactly three decimal places."))
+ assert se_invalid_value(0, 0, num_str) == InvalidValue(
+ 0, 0, num_str, (
+ f"Invalid value '{num_str}'. Expected string representing a number "
+ "with at least six decimal places."))
+
+@given(num_str=st.from_regex(
+ r"^[0-9]+\.([0-9]{1,2}|[0-9]{4,}$)", fullmatch=True))
+def test_cell_average_value_errors_if_not_three_decimal_places2(num_str):
+ """
+ GIVEN: `num_str` is a string representing a number with less than or more
+ than three decimal places, e.g. 2.92, 39.483732
+ WHEN: `num_str` is provided as an argument to `avg_invalid_value` function,
+ THEN: `avg_invalid_value` returns a `quality_control.errors.InvalidValue`
+ object with the information about the placement of the invalid value.
+ """
+ line, col = randint(0, 100), randint(0, 20)
+ assert avg_invalid_value(line, col, num_str) == InvalidValue(
+ line, col, num_str, (
+ f"Invalid value '{num_str}'. Expected string representing a number "
+ "with exactly three decimal places."))
+
+@given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{3}$", fullmatch=True))
+def test_cell_average_value_pass_if_three_decimal_places(num_str):
+ """
+ GIVEN: `num_str` is a string representing a number with exactly three
+ decimal places, e.g. 2.924, 39.483
+ WHEN: `num_str` is provided as an argument to `avg_invalid_value` function,
+ THEN: `avg_invalid_value` returns `None`
+ """
+ line, col = randint(0, 100), randint(0, 20)
+ assert avg_invalid_value(line, col, num_str) is None
+
+@given(num_str=st.from_regex(r"^[0-9]+\.([0-9]{0,5}$)", fullmatch=True))
+def test_cell_standard_error_value_errors_if_less_than_six_decimal_places2(num_str):
+ """
+ GIVEN: `num_str` is a string representing a number with less than six
+ decimal places, e.g. 2.9, 39.4837
+ WHEN: `num_str` is provided as an argument to `se_invalid_value` function,
+ THEN: `se_invalid_value` returns a `quality_control.errors.InvalidValue`
+ object with the information about the placement of the invalid value.
+ """
+ line, col = randint(0, 100), randint(0, 20)
+ assert se_invalid_value(line, col, num_str) == InvalidValue(
+ line, col, num_str, (
+ f"Invalid value '{num_str}'. Expected string representing a number "
+ "with at least six decimal places."))
+
+
+@given(num_str=st.from_regex(r"^[0-9]+\.[0-9]{6,}$", fullmatch=True))
+def test_cell_standard_error_value_pass_if_six_or_more_decimal_places(num_str):
+ """
+ GIVEN: `num_str` is a string representing a number with six or more
+ decimal places, e.g. 2.938434, 39.4837343
+ WHEN: `num_str` is provided as an argument to `se_invalid_value` function,
+ THEN: `se_invalid_value` returns `None`
+ """
+ line, col = randint(0, 100), randint(0, 20)
+ assert se_invalid_value(line, col, num_str) is None
diff --git a/tests/qc/test_header.py b/tests/qc/test_header.py
index 6ca9376..f860a71 100644
--- a/tests/qc/test_header.py
+++ b/tests/qc/test_header.py
@@ -4,7 +4,10 @@ from hypothesis import given
from hypothesis import strategies as st
from quality_control.headers import valid_header
+from quality_control.errors import InvalidValue, DuplicateHeading
from quality_control.errors import DuplicateHeader, InvalidHeaderValue
+from quality_control.headers import (
+ invalid_header, invalid_headings, duplicate_headings)
@given(headers=st.lists(st.text(max_size=10)))
def test_valid_header_errors_with_invalid_headers(headers):
@@ -31,3 +34,58 @@ def test_valid_header_fails_with_duplicate_headers(strains, headers):
"""Check that parsing fails if any header is duplicated"""
with pytest.raises(DuplicateHeader):
valid_header(strains, headers)
+
+## ============================================================
+
+@given(headers=st.lists(st.text(max_size=10), max_size=1))
+def test_invalid_header_with_list_of_one_value(headers):
+ assert invalid_header(0, headers) == InvalidValue(
+ 0, 0, "<TAB>".join(headers),
+ "The header MUST contain at least 2 columns")
+
+@given(headings=st.lists(st.text(min_size=2, max_size=10), min_size=2))
+def test_invalid_headings_with_invalid_inputs(headings):
+ "Verify that the check for header validity works"
+ assert invalid_headings(0, ("BXD1", "BXD2", "BXD3"), headings) == tuple(
+ InvalidValue(0, col, heading, f"'{heading}' not a valid strain.")
+ for col, heading in enumerate(headings, start=2))
+
+@pytest.mark.parametrize(
+ "strains,headers", [
+ (("BXD1", "BXD2", "BXD3"), ("ProbeSet", "BXD3", "BXD1")),
+ (("AStrain", "AnotherStrain", "YetAnotherStrain"),
+ ("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain"))])
+def test_invalid_header_with_valid_headers(strains, headers):
+ "Verify that the check for header validity works"
+ assert invalid_header(0, headers) == None
+
+@pytest.mark.parametrize(
+ "strains,headings", [
+ (("BXD1", "BXD2", "BXD3"), ("BXD3", "BXD1")),
+ (("AStrain", "AnotherStrain", "YetAnotherStrain"),
+ ("AStrain", "AnotherStrain", "YetAnotherStrain"))])
+def test_invalid_headings_with_valid_headings(strains, headings):
+ "Verify that the check for header validity works"
+ assert invalid_headings(0, strains, headings) == tuple()
+
+@pytest.mark.parametrize(
+ "headers,repeated", [
+ (("ProbeSet", "BXD3", "BXD1", "BXD1"), {"BXD1": (3, 4)}),
+ (("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain",
+ "AStrain"), {"AStrain": (2, 5)})])
+def test_duplicate_headers_with_repeated_column_headings(headers, repeated):
+ """Check that parsing fails if any header is duplicated"""
+ assert duplicate_headings(0, headers) == tuple(
+ DuplicateHeading(0, head, cols, (
+ f"Heading '{head}', is repeated in columns "
+ f"{','.join(str(i) for i in cols)}"))
+ for head, cols in repeated.items())
+
+@pytest.mark.parametrize(
+ "headers", [
+ (("ProbeSet", "BXD3", "BXD1")),
+ (("Individual", "AStrain", "AnotherStrain", "YetAnotherStrain",))])
+def test_duplicate_headers_with_unique_column_headings(headers):
+ """Check that parsing fails if any header is duplicated"""
+ assert duplicate_headings(0, headers) == tuple()
+
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-26 12:52:26 +0000