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import pytest
from quality_control.parsing import take, FileType, parse_errors
from quality_control.parsing import collect_errors
@pytest.mark.slow
@pytest.mark.parametrize(
"filepath,filetype,seek_pos",
(("tests/test_data/average_crlf.tsv", FileType.AVERAGE, 0),
("tests/test_data/average_error_at_end_200MB.tsv", FileType.AVERAGE,
205500004 # Skip first 500K lines
),
("tests/test_data/average.tsv", FileType.AVERAGE, 0),
("tests/test_data/standarderror_1_error_at_end.tsv",
FileType.STANDARD_ERROR, 0),
("tests/test_data/standarderror.tsv", FileType.STANDARD_ERROR, 0),
("tests/test_data/duplicated_headers_no_data_errors.tsv",
FileType.AVERAGE, 0)))
def test_parse_errors(filepath, filetype, strains, seek_pos):
"""
Check that only errors are returned, and that certain properties hold for
said errors.
"""
for error in parse_errors(filepath, filetype, strains, seek_pos):
assert isinstance(error, dict)
assert "filepath" in error
assert "filetype" in error
assert "position" in error
assert "error" in error and isinstance(error["error"], str)
assert "message" in error
@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):
taken = take(sample, num)
assert len(taken) <= num
assert taken == expected
## ==================================================
@pytest.mark.slow
@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):
assert len(collect_errors(filepath, filetype, strains, count)) <= count
|
