Added test cases for replace_cgmlst_errors function

tests/parse/test_typing.py

@@ -0,0 +1,71 @@
+"""Test typing method parsing."""
+
+import pytest
+from prp.parse.typing import replace_cgmlst_errors
+from prp.models.typing import ChewbbacaErrors
+
+# build test cases for handeling chewbacca allele caller errors and annotations
+# reference, https://chewbbaca.readthedocs.io/en/latest/user/modules/AlleleCall.html
+cgmlst_test_base = [("1", 1), ("99", 99)]  # normal alllale calls
+cgmlst_test_include_novel = [("INF-1", 1), ("INF-99", 99)]  # inferred alleles
+cgmlst_test_not_include_novel = [
+    ("INF-1", "INF-1"),
+    ("INF-99", "INF-99"),
+]  # inferred alleles
+cgmlst_test_replace_errors = [
+    (err.value, None) for err in ChewbbacaErrors
+]  # errors to strip
+cgmlst_test_not_replace_errors = [
+    (err.value, err.value) for err in ChewbbacaErrors
+]  # errors to strip
+
+
+@pytest.mark.parametrize(
+    "called_allele,expected",
+    [
+        *cgmlst_test_base,
+        *cgmlst_test_not_include_novel,
+        *cgmlst_test_not_replace_errors,
+    ],
+)
+def test_replace_cgmlst_errors_not_include_novel(called_allele, expected):
+    """Test function that process Chewbbaca allele calling."""
+
+    assert (
+        replace_cgmlst_errors(
+            called_allele, include_novel_alleles=False, correct_alleles=False
+        )
+        == expected
+    )
+
+
+@pytest.mark.parametrize(
+    "called_allele,expected",
+    [*cgmlst_test_base, *cgmlst_test_include_novel, *cgmlst_test_not_replace_errors],
+)
+def test_replace_cgmlst_errors_include_novel(called_allele, expected):
+    """Test function that process Chewbbaca allele calling."""
+
+    assert (
+        replace_cgmlst_errors(
+            called_allele, include_novel_alleles=True, correct_alleles=False
+        )
+        == expected
+    )
+
+
+@pytest.mark.parametrize(
+    "called_allele,expected",
+    [*cgmlst_test_base, *cgmlst_test_include_novel, *cgmlst_test_replace_errors],
+)
+def test_replace_cgmlst_errors_include_novel_and_correct_allels(
+    called_allele, expected
+):
+    """Test function that process Chewbbaca allele calling."""
+
+    assert (
+        replace_cgmlst_errors(
+            called_allele, include_novel_alleles=True, correct_alleles=True
+        )
+        == expected
+    )