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-rw-r--r--r_qtl/r_qtl2.py35
-rw-r--r--tests/r_qtl/test_files/nonexistent.zipbin0 -> 380 bytes
-rw-r--r--tests/r_qtl/test_r_qtl2_nonexistent_file.py29
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 differ
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))