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authorFrederick Muriuki Muriithi2024-02-08 04:00:20 +0300
committerFrederick Muriuki Muriithi2024-02-08 04:00:20 +0300
commit1b61b59dcc8e92cbeaedfa7183df281555ba2828 (patch)
treeba7b12b1ba1b753184333d5a1abc3990db59ce04 /tests/r_qtl
parent824ccc82d074c57052972ef676ecf598781ca7e4 (diff)
downloadgn-uploader-1b61b59dcc8e92cbeaedfa7183df281555ba2828.tar.gz
Use error objects rather than plain tuple values.
Diffstat (limited to 'tests/r_qtl')
-rw-r--r--tests/r_qtl/test_r_qtl2_qc.py21
1 files changed, 12 insertions, 9 deletions
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index 1c96a86..554cfc4 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -6,6 +6,9 @@ from zipfile import ZipFile
from r_qtl import r_qtl2 as rqtl2
from r_qtl import r_qtl2_qc as rqc
+from r_qtl.fileerrors import MissingFile
+
+from quality_control.errors import InvalidValue
@pytest.mark.unit_test
@pytest.mark.parametrize(
@@ -85,13 +88,13 @@ def test_missing_files(filepath, expected):
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/empty_control_file_yaml.zip",
- ((None, None, "Missing 'geno' file."),)),
+ (MissingFile("geno", None, "Missing 'geno' file 'None'."),)),
("tests/r_qtl/test_files/test_geno.zip",
tuple()),
("tests/r_qtl/test_files/geno_with_missing_genotypes.zip",
- ((1, "AXR-1", "Invalid value 'X'. Expected one of ('L', 'C')"),
- (2, "EC.480C", "Invalid value 'Y'. Expected one of ('L', 'C')"),
- (6, "HH.335C-Col/PhyA", f"Invalid value 'H'. Expected one of ('L', 'C')")))))
+ (InvalidValue(1, "AXR-1", "X", "Invalid value 'X'. Expected one of ('L', 'C')."),
+ InvalidValue(2, "EC.480C", "Y", "Invalid value 'Y'. Expected one of ('L', 'C')."),
+ InvalidValue(6, "HH.335C-Col/PhyA", "H", f"Invalid value 'H'. Expected one of ('L', 'C').")))))
def test_geno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle
@@ -106,14 +109,14 @@ def test_geno_errors(filepath, expected):
@pytest.mark.parametrize(
"filepath,expected",
(("tests/r_qtl/test_files/empty_control_file_yaml.zip",
- ((None, None, "Missing 'pheno' file."),)),
+ (MissingFile("pheno", None, "Missing 'pheno' file 'None'."),)),
("tests/r_qtl/test_files/pheno_without_errors.zip",
tuple()),
("tests/r_qtl/test_files/pheno_with_errors.zip",
- ((1, "liver", ("Invalid value '61.92'. Expected numerical value "
- "with at least 3 decimal places.")),
- (2, "spleen", ("Invalid value 'brrr'. Expected numerical value "
- "with at least 3 decimal places."))))))
+ (InvalidValue(1, "liver", "61.92", ("Invalid value '61.92'. Expected numerical value "
+ "with at least 3 decimal places.")),
+ InvalidValue(2, "spleen", "brrr", ("Invalid value 'brrr'. Expected numerical value "
+ "with at least 3 decimal places."))))))
def test_pheno_errors(filepath, expected):
"""
GIVEN: A R/qtl2 bundle