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"""Test the parsing of the files"""
import pytest
from quality_control.errors import ParseError
from quality_control.parsing import FileType, parse_file
@pytest.mark.parametrize(
"filepath,filetype",
(("tests/test_data/average_crlf.tsv", FileType.STANDARD_ERROR),
("tests/test_data/average_error_at_end_200MB.tsv",
FileType.STANDARD_ERROR),
("tests/test_data/average.tsv", FileType.STANDARD_ERROR),
("tests/test_data/standarderror_1_error_at_end.tsv", FileType.AVERAGE),
("tests/test_data/standarderror.tsv", FileType.AVERAGE),
("tests/test_data/duplicated_headers_no_data_errors.tsv",
FileType.STANDARD_ERROR),))
def test_parse_file_fails_with_wrong_filetype_declaration(filepath, filetype, strains):
"""Check that parsing fails if the wrong file type is declared"""
with pytest.raises(ParseError):
for line in parse_file(filepath, filetype, strains): # pylint: disable=[unused-variable]
pass
@pytest.mark.parametrize(
"filepath,filetype",
(("tests/test_data/no_data_errors.tsv", FileType.AVERAGE),))
def test_parse_file_passes_with_valid_files(filepath, filetype, strains):
"""Check that parsing succeeds with valid files"""
for line in parse_file(filepath, filetype, strains):
assert bool(line)
@pytest.mark.slow
@pytest.mark.parametrize(
"filepath,filetype",
(("tests/test_data/average_large_no_errors.tsv", FileType.AVERAGE),
# ("tests/test_data/average_no_errors.tsv", FileType.AVERAGE),
# ("tests/test_data/standarderror_no_errors.tsv", FileType.STANDARD_ERROR),
))
def test_parse_file_works_with_large_files(filepath, filetype, strains):
"""Check that parsing succeeds even with large files."""
for line in parse_file(filepath, filetype, strains):
assert bool(line)
@pytest.mark.slow
@pytest.mark.parametrize(
"filepath,filetype",
(("tests/test_data/average_error_at_end_200MB.tsv", FileType.AVERAGE),
("tests/test_data/standarderror_1_error_at_end.tsv", FileType.STANDARD_ERROR),
("tests/test_data/duplicated_headers_no_data_errors.tsv", FileType.AVERAGE)))
def test_parse_file_raises_exception_on_error_in_file(filepath, filetype, strains):
"Check that parsing fails if any error is found in a file"
with pytest.raises(ParseError):
for line in parse_file(filepath, filetype, strains): # pylint: disable=[unused-variable]
pass
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