diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 35 | ||||
| -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 |
3 files changed, 48 insertions, 16 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index a8958a0..d3a3805 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -189,23 +189,26 @@ def file_data(zfile: ZipFile, [str, tuple[str, ...], tuple[str, ...]], tuple[dict, ...]] = __default_process_value_transposed__) -> Iterator[dict]: """Load data from files in R/qtl2 zip bundle.""" - if isinstance(cdata[member_key], list): - for row in (line for lines in - (file_data( - zfile, member_key, {**cdata, member_key: innerfile}, - process_value, process_transposed_value) - for innerfile in cdata[member_key]) - for line in lines): - yield row - return - if not cdata.get(f"{member_key}_transposed", False): - for row in with_non_transposed(zfile, member_key, cdata, process_value): - yield row - return + try: + if isinstance(cdata[member_key], list): + for row in (line for lines in + (file_data( + zfile, member_key, {**cdata, member_key: innerfile}, + process_value, process_transposed_value) + for innerfile in cdata[member_key]) + for line in lines): + yield row + return + if not cdata.get(f"{member_key}_transposed", False): + for row in with_non_transposed(zfile, member_key, cdata, process_value): + yield row + return - for row in with_transposed( - zfile, member_key, cdata, process_transposed_value): - yield row + for row in with_transposed( + zfile, member_key, cdata, process_transposed_value): + yield row + except KeyError as exc: + raise InvalidFormat(*exc.args) from exc def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: """Load cross information where present.""" diff --git a/tests/r_qtl/test_files/nonexistent.zip b/tests/r_qtl/test_files/nonexistent.zip new file mode 100644 index 0000000..4a31bf1 --- /dev/null +++ b/tests/r_qtl/test_files/nonexistent.zip Binary files differdiff --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)) |