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| author | Frederick Muriuki Muriithi | 2024-01-09 09:50:18 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-01-09 09:50:18 +0300 |
| commit | 5491da18dda8c6f55bc2bc5d95f21b86908cd382 (patch) | |
| tree | 6f8224a9056e18b855a2240ae0b8dd24c02f10a5 /tests/r_qtl | |
| parent | b3f5a89aca45a3e803e7bc3b2ee1a3d048801eee (diff) | |
| download | gn-uploader-5491da18dda8c6f55bc2bc5d95f21b86908cd382.tar.gz | |
Raise exception on reading non-existing file
The validation checks ensure that whatever files are listed in the
control file exist in the zip file bundle. It is still possible,
however, that the code tries to read a file that does not exist in the
file and is not listed in the control file. In those cases, raise the
appropriate exception.
Diffstat (limited to 'tests/r_qtl')
| -rw-r--r-- | tests/r_qtl/test_files/nonexistent.zip | bin | 0 -> 380 bytes | |||
| -rw-r--r-- | tests/r_qtl/test_r_qtl2_nonexistent_file.py | 29 |
2 files changed, 29 insertions, 0 deletions
diff --git a/tests/r_qtl/test_files/nonexistent.zip b/tests/r_qtl/test_files/nonexistent.zip Binary files differnew file mode 100644 index 0000000..4a31bf1 --- /dev/null +++ b/tests/r_qtl/test_files/nonexistent.zip diff --git a/tests/r_qtl/test_r_qtl2_nonexistent_file.py b/tests/r_qtl/test_r_qtl2_nonexistent_file.py new file mode 100644 index 0000000..c783a76 --- /dev/null +++ b/tests/r_qtl/test_r_qtl2_nonexistent_file.py @@ -0,0 +1,29 @@ +"""Test accessing nonexistent member.""" +from pathlib import Path + +import pytest +from zipfile import ZipFile + +from r_qtl import r_qtl2 as rqtl2 + +@pytest.mark.unit_test +@pytest.mark.parametrize( + "filepath,memberkey", + (("tests/r_qtl/test_files/nonexistent.zip", "geno"), + ("tests/r_qtl/test_files/nonexistent.zip", "founder_geno"), + ("tests/r_qtl/test_files/nonexistent.zip", "pheno"), + ("tests/r_qtl/test_files/nonexistent.zip", "covar"), + ("tests/r_qtl/test_files/nonexistent.zip", "phenocovar"), + ("tests/r_qtl/test_files/nonexistent.zip", "gmap"), + ("tests/r_qtl/test_files/nonexistent.zip", "pmap"))) +def test_loading_nonexistent_file(filepath, memberkey): + """ + GIVEN: A zipfile with a valid control file, but some files mentioned in the + control file do not exist in the zipfile + WHEN: access is made to such missing files + THEN: raise an exception + """ + with (ZipFile(Path(filepath).absolute(), "r") as zfile, + pytest.raises(rqtl2.InvalidFormat)): + cdata = rqtl2.control_data(zfile) + tuple(rqtl2.file_data(zfile, memberkey, cdata)) |