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"""Test that the QC functions work as expected"""
from pathlib import Path
import pytest
from zipfile import ZipFile
from r_qtl import r_qtl2 as rqtl2
from r_qtl import r_qtl2_qc as qc
###### DO NOT COMMIT THIS ######
from quality_control.debug import __pk__
###### END: DO NOT COMMIT THIS ######
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/empty_control_file_yaml.zip",
tuple()),
("tests/r_qtl/test_files/empty_control_file_json.zip",
tuple()),
("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip",
("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv",
"gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")),
("tests/r_qtl/test_files/allfilesmissing_listmembers.zip",
("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
"pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv",
"phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv",
"phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv",
"phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
"crossinfo01.csv", "crossinfo02.csv")),
("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip",
("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
"pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
"gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
"phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
"crossinfo.csv")),
("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip",
("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
"pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
"gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
"phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
"crossinfo.csv"))))
def test_bundle_files_list(filepath, expected):
"""
GIVEN: R/qtl2 bundle with a control file listing files
WHEN: `bundle_files_list` is called on the bundle
THEN: verify that ALL files listed in the control file are returned.
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
assert qc.bundle_files_list(rqtl2.control_data(zfile)) == expected
@pytest.mark.unit_test
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/empty_control_file_yaml.zip",
tuple()),
("tests/r_qtl/test_files/empty_control_file_json.zip",
tuple()),
("tests/r_qtl/test_files/allfilesmissing_stringmembers.zip",
("geno.csv", "fgeno.csv", "pheno.csv", "covar.csv", "phenocovar.csv",
"gmap.csv", "pmap.csv", "phenose.csv", "sex.csv", "crossinfo.csv")),
("tests/r_qtl/test_files/allfilesmissing_listmembers.zip",
("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
"pheno01.csv", "pheno02.csv", "covar01.csv", "covar02.csv",
"phenocovar01.csv", "phenocovar02.csv", "phenocovar03.csv",
"phenocovar04.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv",
"phenose01.csv", "phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
"crossinfo01.csv", "crossinfo02.csv")),
("tests/r_qtl/test_files/allfilesmissing_mixedmembers.zip",
("geno01.csv", "geno02.csv", "fgeno01.csv", "fgeno02.csv", "fgeno03.csv",
"pheno01.csv", "pheno02.csv", "covar.csv", "phenocovar.csv",
"gmap01.csv", "gmap02.csv", "pmap01.csv", "pmap02.csv", "phenose01.csv",
"phenose02.csv", "sex01.csv", "sex02.csv", "sex03.csv",
"crossinfo.csv")),
("tests/r_qtl/test_files/somefilesmissing_mixedmembers.zip",
("fgeno01.csv", "covar.csv", "gmap01.csv", "gmap02.csv", "pmap01.csv",
"pmap02.csv", "phenose02.csv", "sex03.csv", "crossinfo.csv"))))
def test_missing_files(filepath, expected):
"""
GIVEN: R/qtl2 bundle with a control file listing files
WHEN: `missing_files` is called on the bundle
THEN: verify that ALL files listed in the control file, that do not actually
exist in the bundle are returned.
"""
with ZipFile(Path(filepath).absolute(), "r") as zfile:
assert qc.missing_files(zfile) == expected
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