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
53
54
55
56
57
|
"""Check that error collection works as expected"""
import pytest
from quality_control.parsing import take, FileType, collect_errors
from quality_control.errors import (
InvalidValue, DuplicateHeading, InconsistentColumns)
@pytest.mark.unit_test
@pytest.mark.parametrize(
"sample,num,expected",
((range(0,25), 5, [0, 1, 2, 3, 4]),
([0, 1, 2, 3], 200, [0, 1, 2, 3]),
(("he", "is", "a", "lovely", "boy"), 3, ["he", "is", "a"])))
def test_take(sample, num, expected):
"""Check that `take` works correctly."""
taken = take(sample, num)
assert len(taken) <= num
assert taken == expected
@pytest.mark.slow
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,filetype,count",
(("tests/test_data/average_crlf.tsv", FileType.AVERAGE, 10),
("tests/test_data/average_error_at_end_200MB.tsv", FileType.AVERAGE,
20),
("tests/test_data/average.tsv", FileType.AVERAGE, 5),
("tests/test_data/standarderror_1_error_at_end.tsv",
FileType.STANDARD_ERROR, 13),
("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR, 9),
("tests/test_data/duplicated_headers_no_data_errors.tsv",
FileType.AVERAGE, 10)))
def test_collect_errors(filepath, filetype, strains, count):
"""Check that `collect_errors` works as expected."""
results = take(collect_errors(filepath, filetype, strains), count)
def __valid_instance(item):
return isinstance(item, (InvalidValue, DuplicateHeading))
assert all(__valid_instance(error) for error in results)
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,filetype,expected",
(("tests/test_data/average_inconsistent_columns.tsv", FileType.AVERAGE,
(InconsistentColumns(
4, 4, 5, "Header row has 4 columns while row 4 has 5 columns"),
InconsistentColumns(
5, 4, 3, "Header row has 4 columns while row 5 has 3 columns"),
InconsistentColumns(
6, 4, 7, "Header row has 4 columns while row 6 has 7 columns"))),))
def test_collect_inconsistent_column_errors(filepath, filetype, strains, expected):
"""
Given: A file with inconsistent columns in certain lines
When: collect_errors is run on the file
Then: All the lines with inconsistent columns are flagged
"""
assert tuple(collect_errors(filepath, filetype, strains)) == expected
|
