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path: root/tests/qc/test_error_collection.py
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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