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author | Frederick Muriuki Muriithi | 2022-04-21 10:24:29 +0300 |
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committer | Frederick Muriuki Muriithi | 2022-04-21 10:24:29 +0300 |
commit | d70dbd0addb861aa37c2f2574a537319a75411c7 (patch) | |
tree | fc29c01279a5a1d6485e9dcf44c6d169dddfc73a /tests | |
parent | 7b3dc9d36de1db28a6f36b03de85cf7f527231cc (diff) | |
download | gn-uploader-d70dbd0addb861aa37c2f2574a537319a75411c7.tar.gz |
Collect all the errors
Build a function to collect all the parsing errors into a "sequence"
of dict objects containing the issues found.
Diffstat (limited to 'tests')
-rw-r--r-- | tests/qc/test_error_collection.py | 30 |
1 files changed, 30 insertions, 0 deletions
diff --git a/tests/qc/test_error_collection.py b/tests/qc/test_error_collection.py new file mode 100644 index 0000000..c45803a --- /dev/null +++ b/tests/qc/test_error_collection.py @@ -0,0 +1,30 @@ +import pytest + +from quality_control.parsing import FileType, parse_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), + )) +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 |