From 1b61b59dcc8e92cbeaedfa7183df281555ba2828 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 8 Feb 2024 04:00:20 +0300
Subject: Use error objects rather than plain tuple values.

---
 tests/r_qtl/test_r_qtl2_qc.py | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

(limited to 'tests/r_qtl')

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
-- 
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