From b59ddf47a8f968e23aae6985986806ad5d704474 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Tue, 6 Feb 2024 06:01:35 +0300
Subject: Check that pheno values are numerical and at least 3 decimal places

---
 tests/r_qtl/test_files/pheno_with_errors.zip    | Bin 0 -> 522 bytes
 tests/r_qtl/test_files/pheno_without_errors.zip | Bin 0 -> 539 bytes
 tests/r_qtl/test_r_qtl2_qc.py                   |  30 +++++++++++++++++++-----
 3 files changed, 24 insertions(+), 6 deletions(-)
 create mode 100644 tests/r_qtl/test_files/pheno_with_errors.zip
 create mode 100644 tests/r_qtl/test_files/pheno_without_errors.zip

(limited to 'tests')

diff --git a/tests/r_qtl/test_files/pheno_with_errors.zip b/tests/r_qtl/test_files/pheno_with_errors.zip
new file mode 100644
index 0000000..321e44d
Binary files /dev/null and b/tests/r_qtl/test_files/pheno_with_errors.zip differ
diff --git a/tests/r_qtl/test_files/pheno_without_errors.zip b/tests/r_qtl/test_files/pheno_without_errors.zip
new file mode 100644
index 0000000..9d9d027
Binary files /dev/null and b/tests/r_qtl/test_files/pheno_without_errors.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index bcbcbac..1c96a86 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -7,10 +7,6 @@ from zipfile import ZipFile
 from r_qtl import r_qtl2 as rqtl2
 from r_qtl import r_qtl2_qc as rqc
 
-###### DO NOT COMMIT THIS ######
-from quality_control.debug import __pk__
-###### END: DO NOT COMMIT THIS ######
-
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
     "filepath,expected",
@@ -93,8 +89,8 @@ def test_missing_files(filepath, expected):
      ("tests/r_qtl/test_files/test_geno.zip",
       tuple()),
      ("tests/r_qtl/test_files/geno_with_missing_genotypes.zip",
-      ((1, "AXR-1", f"Invalid value 'X'. Expected one of ('L', 'C')"),
-       (2, "EC.480C", f"Invalid value 'Y'. Expected one of ('L', 'C')"),
+      ((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')")))))
 def test_geno_errors(filepath, expected):
     """
@@ -105,3 +101,25 @@ def test_geno_errors(filepath, expected):
     """
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
         assert tuple(rqc.geno_errors(zfile)) == expected
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
+      ((None, None, "Missing 'pheno' file."),)),
+     ("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."))))))
+def test_pheno_errors(filepath, expected):
+    """
+    GIVEN: A R/qtl2 bundle
+    WHEN: we check for pheno errors
+    THEN: We should get a sequence of all errors present in the pheno file, or
+        an empty sequence if no errors exist.
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert tuple(rqc.pheno_errors(zfile)) == expected
-- 
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