From 3f879d120f7628646f383a457206b15037cc57dc Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 15:18:44 +0300
Subject: Check that data in geno file is valid

Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
---
 .../test_files/geno_with_missing_genotypes.zip     | Bin 0 -> 738 bytes
 tests/r_qtl/test_r_qtl2_qc.py                      |  27 ++++++++++++++++++---
 2 files changed, 24 insertions(+), 3 deletions(-)
 create mode 100644 tests/r_qtl/test_files/geno_with_missing_genotypes.zip

(limited to 'tests/r_qtl')

diff --git a/tests/r_qtl/test_files/geno_with_missing_genotypes.zip b/tests/r_qtl/test_files/geno_with_missing_genotypes.zip
new file mode 100644
index 0000000..b174d4e
Binary files /dev/null and b/tests/r_qtl/test_files/geno_with_missing_genotypes.zip differ
diff --git a/tests/r_qtl/test_r_qtl2_qc.py b/tests/r_qtl/test_r_qtl2_qc.py
index 9b19ae2..bcbcbac 100644
--- a/tests/r_qtl/test_r_qtl2_qc.py
+++ b/tests/r_qtl/test_r_qtl2_qc.py
@@ -5,7 +5,7 @@ import pytest
 from zipfile import ZipFile
 
 from r_qtl import r_qtl2 as rqtl2
-from r_qtl import r_qtl2_qc as qc
+from r_qtl import r_qtl2_qc as rqc
 
 ###### DO NOT COMMIT THIS ######
 from quality_control.debug import __pk__
@@ -47,7 +47,7 @@ def test_bundle_files_list(filepath, expected):
     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
+        assert rqc.bundle_files_list(rqtl2.control_data(zfile)) == expected
 
 @pytest.mark.unit_test
 @pytest.mark.parametrize(
@@ -83,4 +83,25 @@ def test_missing_files(filepath, expected):
         exist in the bundle are returned.
     """
     with ZipFile(Path(filepath).absolute(), "r") as zfile:
-        assert qc.missing_files(zfile) == expected
+        assert rqc.missing_files(zfile) == expected
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "filepath,expected",
+    (("tests/r_qtl/test_files/empty_control_file_yaml.zip",
+      ((None, None, "Missing 'geno' file."),)),
+     ("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')"),
+       (6, "HH.335C-Col/PhyA", f"Invalid value 'H'. Expected one of ('L', 'C')")))))
+def test_geno_errors(filepath, expected):
+    """
+    GIVEN: A R/qtl2 bundle
+    WHEN: We call r_qtl.r_qtl2_qc.geno_errors(..) on it
+    THEN: We should get a sequence of all errors present in the file, or an
+        empty sequence if no errors exist.
+    """
+    with ZipFile(Path(filepath).absolute(), "r") as zfile:
+        assert tuple(rqc.geno_errors(zfile)) == expected
-- 
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