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"""Test the parsing of the R/qtl2 bundles with multiple values for file keys."""
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,filekey,expected",
(("tests/r_qtl/test_files/test_geno_multiple.zip",
"geno",
({
"id": "1", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
"EC.66C": 1
}, {
"id": "2", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
"EC.66C": 1
}, {
"id": "3", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": None,
"EC.480C": 1, "EC.66C": 1
}, {
"id": "4", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
"EC.66C": 1
}, {
"id": "5", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
"EC.66C": 2
}, {
"id": "6", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
"EC.66C": 2
}, {
"id": "7", "PVV4": 1, "AXR-1": 1, "HH.335C-Col/PhyA": 1, "EC.480C": 1,
"EC.66C": 1
}, {
"id": "8", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 1,
"EC.66C": 1
}, {
"id": "9", "PVV4": None, "AXR-1": 2, "HH.335C-Col/PhyA": 2,
"EC.480C": 2, "EC.66C": 2
}, {
"id": "10", "PVV4": 2, "AXR-1": 2, "HH.335C-Col/PhyA": 2, "EC.480C": 2,
"EC.66C": 2
})),))
def test_parse_multiple_files(filepath, filekey, expected):
"""Test parsing of files from R/qtl2 bundle where file keys have multiple values.
GIVEN: Path to a zip file with R/qtl2 data
WHEN: we parse the geno file
THEN: ensure that the data we get is as expected
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
cdata = rqtl2.control_data(zfile)
process_fns = (rqtl2.make_process_data_geno(cdata)
if filekey == "geno" else tuple())
assert tuple(rqtl2.file_data(
zfile, filekey, cdata, *process_fns)) == expected
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