clean up test functions

Sage-Bionetworks · Mar 13, 2024 · ccea136 · ccea136
1 parent c678cc3
commit ccea136
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Showing 2 changed files with 17 additions and 21 deletions.
diff --git a/genie_registry/maf.py b/genie_registry/maf.py
@@ -35,7 +35,7 @@ def _check_tsa1_tsa2(df):
         and not df.query("REFERENCE_ALLELE == TUMOR_SEQ_ALLELE2").empty
     ):
         error = (
-            "maf: Contains instances where values in REFERENCE_ALLELE match values in TUMOR_SEQ_ALLELE2. "
+            f"{error}maf: Contains instances where values in REFERENCE_ALLELE match values in TUMOR_SEQ_ALLELE2. "
             "This is invalid. Please correct.\n"
         )
         row_index = df.query("REFERENCE_ALLELE == TUMOR_SEQ_ALLELE2").index.values

diff --git a/tests/test_maf.py b/tests/test_maf.py
@@ -241,26 +241,6 @@ def test_error__check_allele_col():
     assert warning == ""
 
 
-def test_invalid__check_ref_tsa1_tsa2():
-    """Test the scenario in which maf file has TSA1 and TSA2 and fails"""
-    df = pd.DataFrame(
-        dict(
-            REFERENCE_ALLELE=["A", "A", "A"],
-            TUMOR_SEQ_ALLELE1=["B", "B", "B"],
-            TUMOR_SEQ_ALLELE2=["A", "C", "C"],
-        )
-    )
-    error = genie_registry.maf._check_tsa1_tsa2(df)
-    assert error == (
-        "maf: Contains both "
-        "TUMOR_SEQ_ALLELE1 and TUMOR_SEQ_ALLELE2 columns. "
-        "All values in TUMOR_SEQ_ALLELE1 must match all values in "
-        "REFERENCE_ALLELE or all values in TUMOR_SEQ_ALLELE2.\n"
-        "REFERENCE_ALLELE should not equal to TUMOR_SEQ_ALLELE2. "
-        "Please check row: 1.\n"
-    )
-
-
 @pytest.mark.parametrize(
     "test_df,expected_error",
     [
@@ -335,6 +315,21 @@ def test_invalid__check_ref_tsa1_tsa2():
             ),
             "",
         ),
+        (
+            pd.DataFrame(
+                dict(
+                    REFERENCE_ALLELE=["A", "A", "A"],
+                    TUMOR_SEQ_ALLELE1=["B", "B", "B"],
+                    TUMOR_SEQ_ALLELE2=["A", "C", "C"],
+                )
+            ),
+            "maf: Contains both "
+            "TUMOR_SEQ_ALLELE1 and TUMOR_SEQ_ALLELE2 columns. "
+            "All values in TUMOR_SEQ_ALLELE1 must match all values in "
+            "REFERENCE_ALLELE or all values in TUMOR_SEQ_ALLELE2.\n"
+            "maf: Contains instances where values in REFERENCE_ALLELE match values in TUMOR_SEQ_ALLELE2. "
+            "This is invalid. Please correct.\n",
+        ),
     ],
     ids=[
         "matching_tsa1_tsa2",
@@ -344,6 +339,7 @@ def test_invalid__check_ref_tsa1_tsa2():
         "identical_ref_tsa2_missing_tsa1",
         "valid_ref_tsa2_missing_tsa1",
         "missing_tsa2_ref",
+        "invalid_tsa1_identical_ref_tsa2",
     ],
 )
 def test__check_tsa1_tsa2(test_df, expected_error):